[gmx-users] Simulated Annealing

David van der Spoel spoel at xray.bmc.uu.se
Mon Jan 19 09:04:00 CET 2004

On Mon, 2004-01-19 at 08:31, Martina Bertsch, PhD wrote:
> Greetings.
> I would like to perform the following simulated annealing protocol on a 
> GPCR model in vacuum, while keeping the C-alpha atoms of the 
> transmembrane (TM) helices restrained (fixed?):
> 1) Quick heating from 300-600 K in 1 ps with a 1 fs step.
> 2) Equilibration at 600 K for 100 ps.
> 3) Slow cooling to 500 K.
> 4) Equilibration at 500 K for 200 ps.
> 5) Slow cooling to 400 K.
> 6) Equilibration at 400 K for 200 ps.
> 7) Slow cooling to 300 K.
> 8) Equilibration at 300 K for 200 ps with gradual release of the 
> restrained (fixed?) TM C-alpha atoms.
> 9) Minimization of the resulting structure.
> My questions are:
> a) Is there a way to program the whole protocol in a single mdp? Which 
> mdp options do I use?
> In the past, I used a simple SA cooling from 600 to 0 K in 1 ns (see 
> enclosed mdp), but the papers suggest that a more gradual cooling is 
> preferred.
No, right now you have to do multiple simulations.

> 2) During this process, I would like to keep just the transmembrane 
> C-alpha atoms fixed, e.g., C-alpha in residues 6-30, 43-62, etc. Should I:
> make_ndx -f GPCR_postsd.gro -o index.ndx
>  > r 6-30 & a CA
>  > r 43-62 & a CA
> ...
>  >q
> I seem to recall reading that an atom can only belong to one group. Does 
> that mean that I have to split the original [ C-alpha ] into the [ 
> TM_C-alpha ]
You can do this by adding in make_ndx
newgrp & !oldgrp

> and the [nonTM_C-alpha] and delete the original [ C-alpha ] group? 
> Wouldn't that also imply that I should get rid of the [ backbone ] group 
> -- that sounds a bit suspicious?
Not necessary

> 3) Once I obtain the [ TM_C-alpha ] group, how do I fix it in the mdp? 
> Should I just define:
> freeze_groups [TM_C-alpha]
> freeze_dim y y y
> Or, should I prepare a restraint file TM_posres.itp and define 
> -DPOSRES_TM in the mdp?
you can use your index file with the new group and the genpr program to
generate a new posre.itp

Or you can use freezing.

> 4) How would I encode the gradual release of the [TM_C-alpha] group at 
> the last stage of the protocol?
Not implemented, you'd want the force constant of the restraint to go to
zero slowly, but there is no way currently. You can however just use a
lower force constant (by rerunning genpr).
> 5) If I did not want to fix any parts of the structure, how would I 
> obtain the energy and rmsd for parts of the structure (with respect to 
> the beginning structure), e.g., for TM helix 5, TM helix 7, etc?
> I know that I could define groups TM1-TM7 in the index.ndx, and then for 
> the rmsd calculation:
> g_rms -s gpcr_SA.tpr -f gpcr_SA.trr -o TM7.xvg
> and select the desired group at the prompt.

> I am not sure how to obtain energy profiles for certain groups.
You can specify energy groups in the mdp file. This will give you the
non-bonded bit of the energies, the bonded interactions are summed into
one big lump sum.

David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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