[gmx-users] energy minimization problem

[Justin Lemkul]

On 5/15/15 9:32 AM, Ming Tang wrote:
> Reducing time helps it run longer. But 0.02ps-0.04ps is believed to be reasonable according to gromacs website. So ijust kept trying 0.02ps
>

The time step will depend on the stability of the system, which in turn depends 
on how well equilibrated it is.  If reducing the time step promotes stability 
during equilibration, that is the most obvious solution.  After equilibrating 
for a while, try increasing the time step.

-Justin

> Sent from my Huawei Mobile
>
> Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> On 5/14/15 10:02 PM, Ming Tang wrote:
>> Hi Justin
>>
>> Here is the .mdp file with position restraints, which I downloaded from the martini tutorial website. It works well with the tutorial and my small triple helix, and the grompp process does not give any warnings. Please help to have a look. Many thanks to you.
>>
>> define           =  -DPOSRES
>> integrator       =  md
>> dt               =  0.02
>
> Have you tried simply reducing the time step?  20 fs may be reasonable for a
> well equilibrated system, but if the run is dying early, then this is the first
> thing I would look at.
>
> -Justin
>
>> nsteps           =  50000
>> nstxout          =  0
>> nstvout          =  0
>> nstlog           =  1000
>> nstxtcout        =  1000
>> xtc-precision    =  10
>> cutoff-scheme    =verlet
>> coulombtype      = reaction-field-zero
>> coulomb-modifier = potential-shift-verlet
>> rcoulomb-switch  =  0.9
>> rcoulomb         =  1.4
>> epsilon_r        =  15
>> vdw-modifier     =  force-switch
>> rvdw-switch      =  0.9
>> rvdw             =  1.4
>> tcoupl           =  v-rescale
>> tc-grps          =  Protein W
>> tau-t            =  1.0 1.0
>> ref-t            =  310 310
>> compressibility  =  3e-4
>> ref-p            =  1.0
>> refcoord_scaling =  all
>> pbc              =  xyz
>>
>> -----Original Message-----
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
>> Sent: Friday, 15 May 2015 11:50 AM
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] energy minimization problem
>>
>>
>>
>> On 5/14/15 9:47 PM, Ming Tang wrote:
>>> Dear Justin,
>>>
>>> I saw it in the terminal.
>>>
>>> Potential Energy  = -6.3682131e+05
>>> Maximum force     =  1.8876091e+02 on atom 1147
>>> Norm of force     =  3.1155257e+00
>>>
>>> But, how can I further minimize my protein?
>>>
>>
>> Minimization is not your problem.  Post a full .mdp file of the run that is failing.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul
>>
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>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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> Gromacs Users mailing list
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================