[gmx-users] Extending the MD

[sun]

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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