[gmx-users] virtusal site setting

[Broadbent, Richard]

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 using say 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.


Richard


On 29/03/2013 06:41, "라지브간디" <rajiv at kaist.ac.kr> 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       0.042880515
>
>
>
>
>
>
>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
>
>Richard 
>
>On 28/03/2013 20:02, "����������" <rajiv at kaist.ac.kr> wrote:
>
>>Dear gmx, 
>> 
>>I would like to set virtual sites for CO molecules with some specific
>>charge. 
>> 
>>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.
>> 
>>Rajiv 
>