[gmx-users] unstable system

[Shima Arasteh]

Yes, some letters were transferred by mistakes to email.
Yes, I am using charmm36. Also the rvdw_switch was correct the same as you wrote 1.0  in last email.

Now, I am wondering what the solution is in such cases of facing such an error? Would you please let me know your suggestions? 

Many thanks for your replies.
   

Sincerely,
Shima


________________________________
 From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Sunday, April 7, 2013 4:46 PM
Subject: Re: [gmx-users] unstable system
 






On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh <shima_arasteh2001 at yahoo.com> wrote:

Hi all,
>
> I have a system of peptide/POPC/water/ions. The energy minimization and NVT steps has passed successfully. I ran NPT step for around 10 ns with restraints of protein and P atoms at first nano seconds and then removing them gradually.
>I tried to go on MDRUN. I did not remove restraint of protein atoms completely and they are still restrained. When I run the mdrun command, I get error of "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" .
>I know this error means an unstable system. When I visualized the written pdb files, I see some popc hydrogen atoms are broken and located between two leaflets which are separated by a gap. The protein seems ok, however I  don't get many pdb files to see.
>
>
>As what I see in Diagnosing unstable system web page,
>1. it would be beneficial if one see what part of the system is unstable in first steps. As I saw, the unstable "POPC hydrogen atoms" are not fine.
>2. The single molecules are supposed to examine in water or vacuum too. I have passed this step successfully.
>3. I have not ignored any warning during the last steps.
>4. And my mdp files to run md is as follow:
>
>integrator    = md       
>dt        = 0.002     
>nsteps        = 5000000   
>
>
>ns_type        = grid       
>nstlist        = 5       
>rlist        = 1.2       
>rlistlong       = 1.4
>rcoulomb    = 1.2       
>rvdw        = 1.2       
>pbc        = xyz       
>vdwtype         = switch
>rvdw_switch     = 0.1
>

What force field are you using? CHARMM? In any case, the value of rvdw_switch does not make any sense. If you're using CHARMM, it should be 1.0.
 
; Parameters for treating bonded interactions
>continuation    = yes      
>constraint_algorithm = LINCS    NCS / SHAKE)
>constraints    = all-bonds    )
>lincs_iter    = 1       
>lincs_order    = 4      
>
>; Parameters for treating electrostatic interactions
>coulombtype    = PME        ; Long range electrostatic interactions treatment (cut-off, Ewald, PME)
>pme_order    = 4        ; Interpolation order for PME (cubic interpolation is represented by 4)
>fourierspacing    = 0.16        ; Maximum grid spacing for FFT grid using PME (nm)
>
>; Temperature coupling parameters
>tcoupl        = Nose-Hoover           
>tc-grps        = Protein_POPC Water_and_ions        ; Define groups to be coupled separately to temperature bath
>tau_t        = 0.5    0.5             ; Group-wise coupling time constant (ps)
>ref_t        = 310     310        ; Group-wise reference temperature (K)
>
>; Pressure coupling parameters
>pcoupl        = Parrinello-Rahman     
>pcoupltype    = semiisotropic           
>tau_p        = 2.0               
>ref_p        = 1.01325 1.01325       
>compressibility = 4.5e-5    4.5e-5    
>
>; Miscellaneous control parameters
>; Dispersion correction
>DispCorr    = EnerPres      
>; Initial Velocity Generation
>gen_vel        = no         
>; Centre of mass (COM) motion removal relative to the specified groups
>nstcomm        = 1           y (steps)
>comm_mode    = Linear      
>comm_grps    =Protein_POPC Water_and_ions    ; COM removal relative to the specified groups
>
> Would you please let me know if these happen due to an improper equilibration? Do I need to extend the NPT step? Would that fix it?
>
>

Aside from the above comment, there is nothing particularly wrong about the .mdp file aside from some odd characters here and there, which I will assume are nothing more than quirks of transferring to an email, as they otherwise would have triggered fatal errors in grompp.

-Justin
-- 

======================================== Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ========================================