Dear Justin
Hello :)
Thanks for your response.
You have mentioned that "Position restraints are applied per [moleculetype], as
indicated
in the topology".
In my topol.top file there are two .itp files included for the two protein
chains. I opened the following file:topol_Protein_chain_A.itp
Here I have :
---------------
[ moleculetype ]
; Name nrexcl
Protein_chain_A 3
---------------
1)))))) The molecultype has not mentioned explicitly protein as it is required
by tc_grps (Protein non-Protein). Does gromacs recognizes (Protein_chain_A) as
protein and so gives special thermostat to it????
=====================================
for the 1RFB protein having two chains, I did energy minimization and then NVT
simulation for 200 ps and then used g_energy command to plot temperature.
using this command line:
g_energy -f nvt.mdp -o temp.xvg and then select 15 0 for temperature::::
Then it gives me temp.xvg output, but some warning are written on the screen.
You can see them below:
------Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Temperature 309.834 0.17 3.51504 0.945045 (K)
You may want to use the -driftcorr flag in order to correct
for spurious drift in the graphs. Note that this is not
a substitute for proper equilibration and sampling!
2----((what is the reason for spurious drist and is it necessary to be
corrected?))
WARNING: nmol = 1, this may not be what you want.
(I do not understand this warning)
Temperature dependent fluctuation properties at T = 309.834.
Heat capacities obtained from fluctuations do *not* include
quantum corrections. If you want to get a more accurate estimate
please use the g_dos program.
3-----(It has mentioned that this program needs alot of memory. Is it really
necessary to do this?)
WARNING: Please verify that your simulations are converged and perform
a block-averaging error analysis (not implemented in g_energy yet)
4------(What should I do for this warning)???
========================================================
5----Although the two chains of my protein are identical, does it make trouble
to have two separate .itp files for them? pdb2gmx with the option (chainsep)
has given these two .itp files to me.
Thanks alot for your valuable time....
Regards
Delara
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: delara aghaie <d_agh...@yahoo.com>; Discussion list for GROMACS users
<gmx-users@gromacs.org>
Sent: Saturday, 16 June 2012, 15:37
Subject: Re: [gmx-users] simulating dimer proteins
On 6/16/12 6:29 AM, delara aghaie wrote:
> 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????
Yes, it does. Position restraints are applied per [moleculetype], as indicated
in the topology.
> 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???
No. See the following:
http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do
-Justin
> 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.abra...@anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users@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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--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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