Force fields from .sgm file

Just Got Here

2:18:38 PM PST - Thu, Jan 23rd 2014
Hello everyone. I'd like to create some additional force fields (FF) for nonstandard molecules, and i don't have enough imagination to specify unique name for every new atom in .par file. (There are about 80 of them.) I've found that FF parameters are listed in .sgm file. And according to "NWChem User Documentation Release 5.1.1" (i hope it is still actual in part "segment file format") i can use it in a way: .sgm file 4.600000 5 4 6 0 0 0 1 1 0.000000 1 C 0 0 0 1 1 CT -0.200000 0.000000 21H 0 0 0 1 1 HC 0.050000 0.000000 32H 0 0 0 1 1 HC 0.050000 0.000000 43H 0 0 0 1 1 HC 0.050000 0.000000 54H 0 0 0 1 1 HC 0.050000 0.000000 1 1 2 0 1 # ^ 1 means to use parameters from the card below 0.209000 2.84512E+05 2 1 3 0 1 # ^ 1 means to use parameters from the card below 0.209000 2.84512E+05 3 1 4 0 1 # ^ 1 means to use parameters from the card below 0.209000 2.84512E+05 4 1 5 0 1 # ^ 1 means to use parameters from the card below 0.209000 2.84512E+05 1 2 1 3 0 0 # ^ 0 means to use parameters from database (.par file ???) ignoring the card below 0.000000 0.00000E+00 2 2 1 4 0 0 0.000000 0.00000E+00 3 2 1 5 0 0 0.000000 0.00000E+00 4 3 1 4 0 0 0.000000 0.00000E+00 5 3 1 5 0 0 0.000000 0.00000E+00 6 4 1 5 0 0 0.000000 0.00000E+00 In this example i changed equilibrium C-H bond length (in par file it is equal to 0.109) in CH4. However, geometry optimization calculation uses parameters from .par file. I didn't find any other ways to force NWChem to use FF from .sgm file. So, the questions are: Am i missing something? Are there any additional keys i am to use? And is it even possible to specify FF parameters in .sgm file in actual version of NWChem? BTW: i use NWChem-6.3

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5:52:10 PM PST - Fri, Jan 31st 2014
Hi, Have you ever tried to follow the instruction from this page? http://nwchemgit.github.io/index.php/QMMM_Appendix#Preparing_QM.2FMM_calculations_from_scrat... There, you could get some idea about how to create new segment for QMMM calculation. Best, Tee Quote:VP Jan 23rd 9:18 pm Hello everyone. I'd like to create some additional force fields (FF) for nonstandard molecules, and i don't have enough imagination to specify unique name for every new atom in .par file. (There are about 80 of them.) I've found that FF parameters are listed in .sgm file. And according to "NWChem User Documentation Release 5.1.1" (i hope it is still actual in part "segment file format") i can use it in a way: .sgm file 4.600000 5 4 6 0 0 0 1 1 0.000000 1 C 0 0 0 1 1 CT -0.200000 0.000000 21H 0 0 0 1 1 HC 0.050000 0.000000 32H 0 0 0 1 1 HC 0.050000 0.000000 43H 0 0 0 1 1 HC 0.050000 0.000000 54H 0 0 0 1 1 HC 0.050000 0.000000 1 1 2 0 1 # ^ 1 means to use parameters from the card below 0.209000 2.84512E+05 2 1 3 0 1 # ^ 1 means to use parameters from the card below 0.209000 2.84512E+05 3 1 4 0 1 # ^ 1 means to use parameters from the card below 0.209000 2.84512E+05 4 1 5 0 1 # ^ 1 means to use parameters from the card below 0.209000 2.84512E+05 1 2 1 3 0 0 # ^ 0 means to use parameters from database (.par file ???) ignoring the card below 0.000000 0.00000E+00 2 2 1 4 0 0 0.000000 0.00000E+00 3 2 1 5 0 0 0.000000 0.00000E+00 4 3 1 4 0 0 0.000000 0.00000E+00 5 3 1 5 0 0 0.000000 0.00000E+00 6 4 1 5 0 0 0.000000 0.00000E+00 In this example i changed equilibrium C-H bond length (in par file it is equal to 0.109) in CH4. However, geometry optimization calculation uses parameters from .par file. I didn't find any other ways to force NWChem to use FF from .sgm file. So, the questions are: Am i missing something? Are there any additional keys i am to use? And is it even possible to specify FF parameters in .sgm file in actual version of NWChem? BTW: i use NWChem-6.3

Just Got Here

3:33:15 AM PST - Sat, Feb 1st 2014

Solved

Hi.

Thanks for your reply.

Of course, I tried to follow these instructions.
The problem is that all parameters are to be listed in .par file.
I don't want to change it. I'd like to specify parameters in .sgm file.

I solved this problem.
So, .sgm file should be^

    4.600000
    5    4    6    0    0    0    1    1
    0.000000
    1 C        0    0    0    1    1
     CT       -0.200000    0.000000
    21H        0    0    0    1    1
     HC        0.050000    0.000000
    32H        0    0    0    1    1
     HC        0.050000    0.000000
    43H        0    0    0    1    1
     HC        0.050000    0.000000
    54H        0    0    0    1    1
     HC        0.050000    0.000000
    1    1    2    0    4
#                       ^ 4 means to use parameters from the card below 
    0.209000 2.84512E+05
    2    1    3    0    4
#                       ^ 4 means to use parameters from the card below 
    0.209000 2.84512E+05
    3    1    4    0    4
#                       ^ 4 means to use parameters from the card below 
    0.209000 2.84512E+05
    4    1    5    0    4
#                       ^ 4 means to use parameters from the card below 
    0.209000  2.84512E+05
    1    2    1    3    0    0
#                            ^ 0 means to use parameters from .par file ignoring the card below 
  0.000000 0.00000E+00
    2    2    1    4    0    0
  0.000000 0.00000E+00
    3    2    1    5    0    0
  0.000000 0.00000E+00
    4    3    1    4    0    0
  0.000000 0.00000E+00
    5    3    1    5    0    0
  0.000000 0.00000E+00
    6    4    1    5    0    0
  0.000000 0.00000E+00

Quote:Tpirojsi Jan 31st 4:52 pm

Hi,

Have you ever tried to follow the instruction from this page?

http://nwchemgit.github.io/index.php/QMMM_Appendix#Preparing_QM.2FMM_calculations_from_scrat...

There, you could get some idea about how to create new segment for QMMM calculation.

Best,
Tee

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