[gmx-users] computing REMD swap proba

[David van der Spoel]

pascal.baillod at epfl.ch wrote:

>Thank you very much, Mark and David!
>
>
>3 more REMD questions if you will..
>
>1) I would like to modify the REMD protocol so that the probability of a swap is
>computed with the potential energy of a subsystem (prot-prot and prot-solvent
>interactions, but no solv-solv).. To do so, I have been studying the routines in
>repl_ex.c. I am tracking back the epot variable, which so far brought me to
>ener[F_EPOT] in md.c. Is there any description, somewhere, of the ener array
>elements I need in order to get the above mentioned protein pot energy? With
>energy groups in the .mdp files, I can compute these protein energies..
>  
>
There is a recent PNAS paper (Berne) about this, but in my opinion it is 
quite useless, since all but one of the replicas are unphysical.

You want to check the summation of energies in src/mdlib/tgroup.c and 
the t_grp_ener data structure.

>2) I tried to recompute the swap probability. I only get the same result as the
>gromacs code if I use the target temperature and not the current simulation
>temperature in the formula, i.e. using the target 300.0 of the mdp input instead
>of using the current 301.2 of the log file for that step. Shouldn't one use the
>current temperature, more representative of the conformation to be exchanged? I
>wonder if there are similar problems for the P*V term (although it is negligible)..
>  
>
No. The fluctuations in T and P should be independent of the exchange 
probability.

>
>3) I still do not manage to get PT running with more than 2 replicas, in the NPT
>ensemble.. For reminder:
>  
>
Is this official 3.3 or an intermediate CVS version?

>I have tried running NPT-REMD with 3 replicas, at 300, 302 and 304 K. My .mdp
>files are identical, with the exception of the target temperature. The log files
>of the aborted simulation also indicate that:
>
>Multi-checking the pressure coupling ... OK
>Repl  There are 3 replicas:
>Repl      0     1     2
>Repl  T 300.0 302.0 304.0
>Repl  p  1.00  1.00  1.00-------------------------------------------------------
>Program mdrun_mpi, VERSION 3.3
>Source code file: repl_ex.c, line: 142
>                                                                               
>                                                                     
>Fatal error:
>The reference pressure decreases with increasing temperature
>-------------------------------------------------------
>
>Could that have something to do with the size of the system (38373 atoms)?
>  
>
No.

>Thanks a lot for any help!!
>
>
>
>Pascal
>
>
>
>
>
>
>
>*******************************************************************************
>Pascal Baillod (PhD student) 
>*******************************************************************************
>Swiss Federal Institute of Technology EPFL	        Tel: +41-(0)21-693-0322
>Institute of Chemical Sciences and Engineering ,	Fax: +41-(0)21-693-0320
>Laboratory of Computational Chemistry and Biochemistry	pascal.baillod at epfl.ch
>Room BCH 4121, Avenue Forel,	                        http://lcbcpc21.epfl.ch
>CH-1015 Lausanne	
>*******************************************************************************
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>  
>


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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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