[gmx-users] Extend the simulation

Justin Lemkul jalemkul at vt.edu
Sun Feb 21 02:23:20 CET 2016



On 2/20/16 8:21 PM, Elsaid Younes wrote:
> Ok, How can I use md_0_1.tpr instead of topol.tpr
>

Your original command:

gmx mdrun -deffnm md_0_1

"Run whatever mdrun you did before, but add -cpi -append."

which means:

gmx mdrun -deffnm md_0_1 -cpi -append

-Justin

> /Elsaid
>
> On Sun, Feb 21, 2016 at 2:59 AM, Elsaid Younes <elkhot at gmail.com> wrote:
>
>> Hi,
>>
>> The mdrun I did was gmx mdrun -deffnm md_0_1
>> I write the command
>>   mdrun -cpi md_0_1_prev.cpt -append
>>   I tried to use -noappend, but still doesn't work.
>>
>> /Elsaid
>>
>> On Sun, Feb 21, 2016 at 2:43 AM, Elsaid Younes <elkhot at gmail.com> wrote:
>>
>>> Still asks for topol.tpr? Can I have that file
>>>
>>>
>>> /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

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


More information about the gromacs.org_gmx-users mailing list