[gmx-users] simulating dimer proteins
Justin A. Lemkul
jalemkul at vt.edu
Sat Jun 16 13:51:00 CEST 2012
On 6/16/12 7:33 AM, delara aghaie wrote:
> Dear Justin
> Hello :)
> Thanks for your response.
> You have mentioned that "Position restraints are applied per [moleculetype], as
> in the topology".
> In my topol.top file there are two .itp files included for the two protein
> chains. I opened the following file:
> Here I have :
> [ moleculetype ]
> ; Name nrexcl
> Protein_chain_A 3
Somewhere above this you will see lines something like the following:
This is the information you need. Both chains should be under the control of
identical #ifdef constructs, so invoking -DPOSRES will take care of all position
> 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????
Whether or not something is recognized as protein depends on the content of
residuetypes.dat, so for normal proteins (regardless of how many there are),
they will be recognized. Each [moleculetype] is not given its own special
thermostat, nor should 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?))
I doubt that warning is relevant.
> 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?)
None of the preceding messages are relevant, and the fact that they are printed
is spurious and will be fixed in the code.
> 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)???
Block averaging is a common analysis used for many observables. It will tell
you if you have trends in your data. For temperature, it should be fairly
obvious just by looking at the graph whether or not it has converged.
> 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.
It's a perfectly reasonable approach, and in fact the easiest since pdb2gmx
takes care of everything for you.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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