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 <elk...@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 <elk...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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