[gmx-users] Umbrella Samling Alteration

[Justin Lemkul]

On 2/8/15 5:53 PM, Alexander Law wrote:
> This method doesn't work. Does each simulation have to complete the 10 ns in order to move on the analysis step, or can I use incomplete simulations?
>

Analyze however much time you like.

> If not, is there another possibility to force the simulations to complete?
>

If by "complete" you mean "terminate ahead of schedule" that's what Ctrl+C or 
whatever queue commands (e.g. qdel) are for.

-Justin

> Thanks,
> Alex
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
> Sent: Friday, February 06, 2015 12:07 AM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Umbrella Samling Alteration
>
> On 2/4/15 7:22 PM, Alexander Law wrote:
>> Hi Justin
>>
>> The runs have started but they are not currently running, as in they were cancelled and I can start them up again using the .cpt file. Is it still possible to alter add the -nsteps in this case?
>>
>
> That should always be possible. Try it and see.
>
> -Justin
>
>> Many Thanks,
>> Alex
>> ________________________________________
>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
>> Sent: Tuesday, February 03, 2015 1:51 AM
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Umbrella Samling Alteration
>>
>> On 2/1/15 11:22 PM, Alexander Law wrote:
>>> Dear Gromacs Users
>>>
>>> I am currently running the series of simulations using the following command:
>>>
>>> mdrun -deffnm umbrella0 -pf pullf-umbrella0.xvg -px pullx-umbrella0.xvg
>>>
>>> I wish to lessen the amount of time for each of these simulations from 10 ns to 6 ns. These simulations are already up to around 5 ns, is it possible to change the time to 6 ns without altering the md_umbrella.mdp file and starting agin? Also, will this reduction have any major impacts on the quality/efficacy of the data?
>>>
>>
>> Use mdrun command-line option -nsteps to override the number of steps specified
>> in the .tpr file, but you can't do this if the runs are in progress.
>>
>> -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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-- 
==================================================

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

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