[gmx-users] Extend the simulation

[Elsaid Younes]

It says:

No previous checkpoint file present, assuming this is a new run.
Reading file md_0_1.tpr, VERSION 5.0.4 (single precision)
Changing nstlist from 10 to 20, rlist from 1 to 1.03

then start......

/Elsaid

On Sun, Feb 21, 2016 at 3:21 AM, Elsaid Younes <elkhot at gmail.com> wrote:

> Ok, How can I use md_0_1.tpr instead of topol.tpr
>
> /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
>>>>>
>>>>
>>>>
>>>
>>
>