[gmx-users] linc warnings

subarna thakur thakur.subarna at yahoo.co.in
Wed Dec 30 08:24:24 CET 2009

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?

From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at 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.


> 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:



> Subarna
> ------------------------------------------------------------------------
> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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