[gmx-users] Setting virtual sites ?

라지브간디 rajiv at kaist.ac.kr
Thu Apr 4 18:40:29 CEST 2013

Dear Richard,

I've included the COM in my .gro and also updated the rtp, atp and ffnonbonded.itp files as well as the exact coefficient value.  But when I use gromp I get the error that COM not found in atom type database .

Actually I included the COM in atomtypes.atp like 
COM  0.0000

As it doesn't have mass value. In addition, I included in ffnonbonded. Itp file by setting their LJ value as 0 ( both sigma and epsilon )

Please suggest how to avoid this error.
Thanks in advance.


Dear Rajiv, 

The .itp looks fine to me except for the coefficient in the virtual site 
which I think should be much closer to 0.5. 

If the issue is that you don't have the coordinate on the COM in your .gro 
file then you will need to generate it yourself. If you have one CO 
molecule which you use to build a box usingsay genconf I would suggest 
just working out the position by hand and modifying the .gro manually. If 
that is not the case (ie. you have many CO molecules at all stages of the 
process) it's time to get out your favourite programming language and 
write a program which reads a .gro and adds the COM to each molecule and 
writes it out again. 


On 29/03/2013 06:41, "" wrote: 
>Dear Richard, 
>For instance, To simulate the hemoglobin with heme ligated CO, would like 
>to set the charges on center of mass of CO. 
>How do i include the virtual sites atom in co-ordinates (x,y and z)?. I 
>added the virtual sites line in topology as follows: 
>[ moleculetype ] 
>; molname nrexcl 
>CMO 2 
>[ atoms ] 
>; id at type res nr residu name at name cg nr charge 
>1 OM 1 CMO O 1 -0.85 15.9994 
>2 CM 1 CMO C 1 -0.75 12.0110 
>3 COM 1 CMO M 1 1.60 0.000 
>[ bonds ] 
>; i j funct length force.c. 
>1 2 1 0.1128 933032.0 
>[ virtual_sites2 ] 
>; Vsite from funct a 
>3 1 2 1 0.5000

>Also, i entered in .atp and .rtp file. Could you please give some 
>procedure to do this? Thanks in advance. 
>Dear Rajiv, 
>Without a clear explanation of what you are doing and the specific error 
>message from grompp it is impossible to offer any sensible advice. 
>Other pieces of information which might be useful would be, the topology 
>file, the actual grompp line, and the gro file for a single CO molecule 
>On 28/03/2013 20:02, "������������������������������" wrote: 
>>Dear gmx, 
>>I would like to set virtual sites for CO molecules with some specific 
>>As per GROMACS manual, I've created virtual site2 in topology file for 
>>CO. Also, given the information in .rtp file as well as added the 
>>COM(center of mass) atom in .gro file. However, when I use gromp, it 
>>shows COM not found. 
>>Please need an advice. Thanks. 


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