[gmx-users] linc warnings

Justin A. Lemkul jalemkul at vt.edu
Wed Dec 30 13:12:24 CET 2009



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 <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.
> 
> <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
>  >
>  > ------------------------------------------------------------------------
>  > The INTERNET now has a personality. YOURS! See your Yahoo! Homepage 
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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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-- 
========================================

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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