subarna thakur wrote:
Hi,
I am using the following keywords in pr.mdp file for the simulation for
protein with fe4s4 cluster;
title = Yo
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = 1500000 ; total 3000 ps.
nstcomm = 1
nstxout = 500
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300
; Energy monitoring
energygrps = Protein Non-Protein
; Pressure coupling is not on
Pcoupl = no
tau_p = 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
But the Fe4s4 cluster atoms are showing large rms and rotating hugely in
position restraining step and Linc warnings are comming.
In some published papers it is mentioned that during the molecular
dynamics simulations, the proteins' heavy atoms and the counter ions
were harmonically restrained to their initial positions of pdb, How can
I do this for my fe4s4 cluster. What keywords should I use for that and
in which step I can do?
That's what position restraints are doing.
Watch the trajectory, and see if you can find where things are going wrong. If
the crash is happening reasonably early, you can set "nstxout = 1" to get a
bunch of frames right before the crash. Perhaps there are some atomic clashes
that are still unresolved after EM. The Fmax you achieved before is indeed
quite high. Have a look around atom 820 and see where the clash might be.
Another possibility for the instability of your system is of course
inappropriate parameters in the topology. How have you parameterized the Fe4S4
cluster? MM force fields generally fail spectacularly for such transition metal
species, especially with the quantum effects (charge transfer, etc) present in
such systems. Have you seen the following?
http://www.gromacs.org/Documentation/How-tos/Parameterization#Exotic_Species
-Justin
subarna
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Sent:* Tue, 29 December, 2009 5:44:03 PM
*Subject:* Re: [gmx-users] linc warnings
subarna thakur wrote:
> Hi
> My protein has a Fe4S4 cluster. I have been able to minimize the
structure using Steepest descent. The log file shows following message:
> Steepest Descents converged to Fmax < 2000 in 372 steps
> Potential Energy = -4.1580605e+06
> Maximum force = 1.7402682e+03 on atom 820
> Norm of force = 3.0794989e+01
> -----------------
> But during the position restraining step, following Linc warning is
coming before stopping all-together
If EM worked nicely, then something else you are doing is incorrect.
<snip>
> the atoms 5437,5438,5439 are the FE atoms of the Fe4S4 cluster. these
atoms are rotating hugely and showing large rms..
> Please suggest how to tackle the FE atoms during simulation run ?
Without the metal cluster, the same protein is working fine under
simulation and there is no such linc warinings?
>
Without seeing your .mdp file and perhaps even snippets of your topology
pertaining to the Fe4S4 cluster, there's nothing else to say except
please read the standard advice:
http://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings
-Justin
> Subarna
>
> ------------------------------------------------------------------------
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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The INTERNET now has a personality. YOURS! See your Yahoo! Homepage
<http://in.rd.yahoo.com/tagline_yyi_1/*http://in.yahoo.com/>.
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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