Hello Juraj,
Thank you for ur suggestion, I applied two strategies
1) used 0.1 nsec. On CPU then addtional 0.1 nsec CPU after that started the GPU (your suggestion and Dr. David as well)
2) I repeated the preparation step with smaller box size 10 A instead of 20 A
Both are okay and simulation now running for both cases.
Thank you Juraj and David
Best regards,
Mohamed Marzouk Sobeh
Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
T.A Physics department,Ain Shams University, Cairo, Egypt.
Emails:
mohamed_marzouk.sci.asu.edu.eg
marzouk.aa.m.titech.ac.jp
marzouk_biophysics.yahoo.com
mohamedmarzoukphysics.gmail.com
Mob. and WhatsApp.:
+81 070-4070-9549
+2 01061417414
> On Oct 8, 2 Reiwa, at 8:21 PM, Juraj Dobias <juraj.dobias.uochb.cas.cz> wrote:
>
> Hello Mohamed,
>
> This is pretty common error and Amber also suggested possible solutions for you. When I receive this error I run 100 ps simulation using CPU code (in my case pmemd.MPI instead of pmemd.cuda) and then continue with GPU. Or alternatively you can start new GPU simulation with generated restart file, but it can fail again. So maybe you will have to do it several times.
>
> best regards,
>
> Juraj
>
> On 08. 10. 20 4:41, mohamed marzouk wrote:
>> This is the error message
>>
>> packet_write_wait: Connection to 133.48.230.17 port 22: Broken pipeo much from their initial values.
>> (base) Mohameds-iMac:~ marzouk$ changed by a large amount, probably from
>> starting the simulation from a structure a long way from equilibrium.
>>
>> [Although this error can also occur if the simulation has blown up for some reason]
>>
>> The GPU code does not automatically reorganize grid cells and thus you
>> will need to restart the calculation from the previous restart file.
>> This will generate new grid cells and allow the calculation to continue.
>> It may be necessary to repeat this restarting multiple times if your system
>> is a long way from an equilibrated density.
>>
>> Alternatively you can run with the CPU code until the density has converged
>> and then switch back to the GPU code.
>>
>> Best regards,
>> Mohamed Marzouk Sobeh
>> Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
>> T.A Physics department,Ain Shams University, Cairo, Egypt.
>> Emails:
>> mohamed_marzouk.sci.asu.edu.eg
>> marzouk.aa.m.titech.ac.jp
>> marzouk_biophysics.yahoo.com
>> mohamedmarzoukphysics.gmail.com
>>
>> Mob. and WhatsApp.:
>> +81 070-4070-9549
>> +2 01061417414
>>
>>
>>
>>
>>
>>> On Oct 8, 2 Reiwa, at 12:17 AM, David A Case <david.case.rutgers.edu> wrote:
>>>
>>> On Wed, Oct 07, 2020, mohamed marzouk wrote:
>>>
>>>> After that, I tried to run NPT with restrain 10 as a first step then I
>>>> will reduce gradually, however couldn’t run the error message photo no. 4
>>> I don't see any photos of error messages. Can you just copy and paste
>>> the error you get into your email?
>>>
>>> ...thanks...dac
>>>
>>>
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Received on Mon Oct 12 2020 - 11:00:02 PDT
