[gmx-users] simulating dimer proteins

[delara aghaie]

Dear Mark
Again some questions:
------------------------------------------
I used -chainsep option to pdb2gmx and generated topology files for two protein chains and also .gro file containing both chains
........................................
The energy minimization was done successfully and I got average pot. energy=-1.2*10^6
Then I started NVT simulation for 200 ps with position restraints on proteins. 

1)) having the following line in .mdp file will do position restraints on both chains, considering that each chan has its own .top file????

define          = -DPOSRES      ; position restrain the protein
---------------------------------
200 ps, NVT simulation finished, but I think there is something wrong here. This is part of my nvt.mdp file:


; Temperature coupling is on
tcoupl          = V-rescale     ; modified Berendsen thermostat
tc-grps         = Protein Non-Protein   ; two coupling groups - more accurate
tau_t           = 0.1   0.1     ; time constant, in ps
ref_t           = 310   310     ; reference temperature, one for each group, in K

As here my protein has two chains, is it necessary to increase the tc-groups??? I mean should I use for example 
tc-grps = Protein_chain_A Protein_chain_B SOl NA     (These are the names that are present at the end of topol.top file)

Thanks
Regards
D.M





________________________________





________________________________


From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Saturday, 16 June 2012, 12:15
Subject: Re: [gmx-users] simulating dimer proteins
 

On 16/06/2012 5:31 PM, delara aghaie wrote: 
Dear Gromacs Users
>
>
>Running pdb2gmx on a pdb file containing a dimer protein, I used option (( chainsep id_or_ter)))
>This resulted in separated topologies for each chain and separated posre files. Also in the .gro file, the aminoacides of the second chain started from number 1. (Without this option the second chain aminoacides will receive numbers in continuation of numbers of first chain))....
>
>
>Now:
>Can I use these files to continue the simulations or again it is necessary to follow the procedure explained in multiple chains gromacs???
>
By definition of pdb2gmx function, you now have a topology and a
    coordinate file that matches. That is the minimum requirement for
    grompp to succeed later. grompp doesn't care about some aspects of
    atom numbering - including your observation above.

Mark

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