[gmx-users] Fwd: [gmx-developers] Simulated annealing problem

[David van der Spoel]

This is a user problem, not a development problem.


-------- Original Message --------
Subject: [gmx-developers] Simulated annealing problem
Date: Thu, 14 Mar 2013 10:15:39 +0530
From: Gaurav Jerath <g.jerath at iitg.ernet.in>
Reply-To: Discussion list for GROMACS development 
<gmx-developers at gromacs.org>
To: gmx-developers at gromacs.org

Hi,
I am trying to anneal two protein molecules.
The usual protocol for a MD simulation was followed.
But the problem arises that at high temperatures, the number of hydrogen
bonds are increasing instead of getting decreased. The GROMOS43a1 force
field was used and the mdp file for the simulation is shown below:


;
title               =  Yo
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002	;ps !
nsteps              =  5000000	; total 10ns.
;nstcomm             =  1
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  100
nstenergy           =  100
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
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        = 300  		300      ; reference temperature, one for each
group, in K
; Energy monitoring
energygrps          =  Protein  SOL
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  2.75
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 310 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529
; SIMULATED ANNEALING CONTROL =
annealing               =  periodic periodic
annealing_npoints        = 3 3
annealing_time          = 0 5000 10000 0 5000 10000
annealing_temp          = 300 500 300 300 500 300


Kindly help me as I am unable to figure out if there is a problem in my
parameters file


-------------- next part --------------
-- 
gmx-developers mailing list
gmx-developers at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-developers
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-developers-request at gromacs.org.