[gmx-users] Extend the simulation

[Elsaid Younes]

Sorry
Once, I added .tpr to the md_0_1 then it gave me the above message then I
did as you said without .tpr.
That error was obtained:

Fatal error:
Can't read 509132 bytes of 'md_0_1.log' to compute checksum. The file has
been replaced or its contents have been modified. Cannot do appending
because of this condition.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

/Elsaid

On Sun, Feb 21, 2016 at 3:38 AM, Elsaid Younes <elkhot at gmail.com> wrote:

> 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
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>