[gmx-users] Extend the simulation

[Justin Lemkul]

On 2/20/16 7:43 PM, Elsaid Younes wrote:
> Still asks for topol.tpr? Can I have that file
>

You already have a .tpr file, otherwise your simulation never would have run.

If you want help, you need to provide (1) the exact mdrun you gave originally 
for the job that stopped prematurely and (2) the exact mdrun command you're 
giving now, trying to re-start it.  It's impossible for anyone on the mailing 
list to tell you exactly what to type because we don't know your file names. 
The relevant options you need to *add* to the previous command are given below. 
  These do not replace previous options or constitute a complete mdrun command.

-Justin

>
> /Elsaid
> On 2/20/16 6:49 PM, Elsaid Younes wrote:
>> * Hi,
> *>>>* If I have this file md_0_1_prev.cpt What is the text exactly? It asks
> *>* for topol.tpr
> *
> I gave you the command-line options that are new to the mdrun command
> line.  Run
> whatever mdrun you did before, but add -cpi -append.  Doing this is a routine
> task, covered on the website and in half a million posts in the archive (Google
> is your friend).
>
> -Justin
>
>> * On 2/20/16 5:32 PM, Elsaid wrote:
> *>>* * The simulation has the time,  which is time of the wanted
> simulation. But the
> *>* *>* job was killed by the server.
> *>* *
> *>* If the simulation terminated prior to completion, you don't need
> to operate on
> *>* the .tpr file at all.  Just continue from the last checkpoint
> *>>* mdrun -cpi -append
> *>>* -Justin*
>
>
> On Sun, Feb 21, 2016 at 1:49 AM, Elsaid Younes <elkhot at gmail.com> wrote:
>
>> Hi,
>>
>>
>> If I have this file md_0_1_prev.cpt What is the text exactly? It asks for topol.tpr
>> On 2/20/16 5:32 PM, Elsaid wrote:
>>> * The simulation has the time,  which is time of the wanted simulation. But the
>> *>* job was killed by the server.
>> *
>> If the simulation terminated prior to completion, you don't need to operate on
>> the .tpr file at all.  Just continue from the last checkpoint
>>
>> mdrun -cpi -append
>>
>> -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 <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> | (410) 706-7441http://mackerell.umaryland.edu/~jalemkul
>>
>>
>>
>> On Sun, Feb 21, 2016 at 12:32 AM, Elsaid <elkhot at gmail.com> wrote:
>>
>>> The simulation has the time,  which is time of the wanted simulation. But
>>> the job was killed by the server.
>>> /Elsaid
>>>
>>
>>

-- 
==================================================

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

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