[gmx-users] energy minimization problem
Ming Tang
m21.tang at qut.edu.au
Sat May 16 14:30:51 CEST 2015
Dear Justin,
I tried to use small time step. First, set dt=0.005ps, after running 20ps, I found one chain of the triple helix just went to another water box totally. I guess there is something wrong with the martini ff because of the small time step.
Then, I increased it to 0.01ps, after running 40ps, I checked the .gro, and found all the three chains stay together, which is reasonable. However, even use dt=0.01, the simulation can only run about 1ns. And, after simulating 100 ps using dt=0.01ps, the simulation can just run thousands of steps when dt is increased to 0.02ps. I tried many times and many different time steps, but still could not see the possibility for it to run hundreds of nanoseconds, which is quite normal when using martini force. If the system can be further minimized, then it can run longer maybe.
Thanks a lot.
-----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 11:38 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] energy minimization problem
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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>>
>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>
--
==================================================
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
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users
mailing list