[gmx-users] Extending the MD

[sun]

Allright Sapna. Thank you very much.

Sent from my iPhone

> On 26-May-2016, at 4:59 pm, SAPNA BORAH <sapnauser365 at gmail.com> wrote:
> 
> I would suggest if you want simulation runs with new name, add the -deffnm
> switch and provide the default name :)
> Saves us from all the trouble to rename the files all over again.
> 
> gmx mdrun -v -s next1.tpr -cpi state.cpt -deffnm new
> 
> 
> Sapna Mayuri Borah
> c/o Dr. A. N. Jha
> Research student
> Tezpur University,
> India
> 
>> On Thu, May 26, 2016 at 4:57 PM, SAPNA BORAH <sapnauser365 at gmail.com> wrote:
>> 
>> It may be a case. You can rename the files to what they were and try
>> again. Since here, the error simply implies the files are renamed or
>> missing.
>> 
>> Sapna Mayuri Borah
>> c/o Dr. A. N. Jha
>> Research student
>> Tezpur University,
>> India
>> 
>>> On Thu, May 26, 2016 at 4:46 PM, sun <sun.iba2 at gmail.com> wrote:
>>> 
>>> Yes
>>> In my case it was state.cpt and used the following command after
>>> generating .tpr:
>>> gmx mdrun -v -s next1.tpr -cpi state.cpt
>>> 
>>> Has it anything to do with trajectory or log files generated in 100 ns
>>> case? I have renamed the .trr and .xtc files generated for 100 ns
>>> simulation.
>>> 
>>> Sent from my iPhone
>>> 
>>>> On 26-May-2016, at 4:43 pm, SAPNA BORAH <sapnauser365 at gmail.com> wrote:
>>>> 
>>>> Well that's kinda new i must say. Can you please paste the entire
>>> command
>>>> you have used. I think you have mis-named the file :).
>>>> 
>>>> By previous.cpt, I mean your last/previous checkpoint file of the
>>>> simulation run, that will be state.cpt in your case.. Hope you have
>>>> mentioned that. Ignore if you have :)
>>>> 
>>>> Sapna Mayuri Borah
>>>> c/o Dr. A. N. Jha
>>>> Research student
>>>> Tezpur University,
>>>> India
>>>> 
>>>>> On Thu, May 26, 2016 at 4:38 PM, sun <sun.iba2 at gmail.com> wrote:
>>>>> 
>>>>> Hello Sapna
>>>>> I tried adding previous.cpt but the following the following error
>>> appears:
>>>>> "One out of the 4 files is either missing or renamed"
>>>>> 
>>>>> 
>>>>> 
>>>>> Sent from my iPhone
>>>>> 
>>>>>> On 26-May-2016, at 4:35 pm, SAPNA BORAH <sapnauser365 at gmail.com>
>>> wrote:
>>>>>> 
>>>>>> Hi!!
>>>>>> 
>>>>>> After converting the tpr, while initiating mdrun, try adding the
>>> previous
>>>>>> cpt file as well..
>>>>>> 
>>>>>> mdrun -s next.tpr -cpi previous.cpt
>>>>>> 
>>>>>> Thanks!
>>>>>> 
>>>>>> 
>>>>>> Sapna Mayuri Borah
>>>>>> c/o Dr. A. N. Jha
>>>>>> Research student
>>>>>> Tezpur University,
>>>>>> India
>>>>>> 
>>>>>>> On Thu, May 26, 2016 at 4:31 PM, sun <sun.iba2 at gmail.com> wrote:
>>>>>>> 
>>>>>>> Hello
>>>>>>> I started a 100 ns ns pro-lig simulation which was terminated
>>> accidently
>>>>>>> at 53.33 ns. Then I restarted simulation with checkpoint file and
>>>>>>> simulation ended at 100 ns. Now I have the md_0_1.tpr and next.tpr
>>> files
>>>>>>> which were generated for 53.33 and 100 ns data reapectively and log,
>>> trr
>>>>>>> file for both 53.33 and 100 ns MD. I have state.cpt, state_prev.cpt,
>>>>>>> md_0_1.cpt. Now i want to extend the simulation upto 200 ns. So i
>>> gave
>>>>> the
>>>>>>> following commands:
>>>>>>> gmx convert-tpr -f md_0_1.tpr -extend 200000 -o next1.tpr
>>>>>>> and
>>>>>>> gmx mdrun -v next1.tpr
>>>>>>> 
>>>>>>> But, the mdrun started from initial step and time 0.00. That means
>>>>>>> simulation is starting from begining and not after 100 ns to 200 ns.
>>> I
>>>>> am
>>>>>>> confused if i am using the right .tpr file or shall I use checkpoint
>>>>> file.
>>>>>>> Same results are obtained when i used next.tpr instead of md_0_1.tpr.
>>>>> When
>>>>>>> i used checkpoint files (all three files in three different steps)
>>> the
>>>>>>> simulation is starting from 53.33 ns. Plz suggest where I am going
>>>>> wrong.
>>>>>>> With Regards
>>>>>>> Suniba
>>>>>>> 
>>>>>>> Sent from my iPhone
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