Hi Lara,
I am not sure I fully follow what you are saying here but are you essentially saying that the following works:
pmemd.cuda -i eq2_pmemd.in -p solvated_protein.prmtop -c eq1.rst -ref eq1.rst -o eq2.log
but
pmemd.cuda -i eq2_pmemd.in -p solvated_protein.prmtop -c eq1.rst -ref eq1.rst -o eq2.log -x eq2_pmemd.mdcrd -r eq2_pmemd.rst
does not and gives you the NRESPA error? - If that is the case it makes no sense at all. There would have to be something very wonky inside your AMBER installation to see behavior like that.
Can you confirm the version of AMBER you are using - did you install it or did someone else? - do you know if the various updates were applied? and if anything was modified in the source code?
All the best
Ross
> On Sep 2, 2015, at 3:17 PM, Lara rajam <lara.4884.gmail.com> wrote:
>
> Dear amber !
>
> It is working , the mistake is mine ! , when I give the run as
>
> pmemd.cuda -i eq2_pmemd.in -p solvated_protein.prmtop -c eq1.rst -ref
> eq1.rst -o eq2.log
>
> I was able to do it and if i give the mdcrd and rest file flags it is
> giving me the problem.
>
> I also understood that the default value for nrespa=1.
>
>
> thank you so much for the reply , but still I have some issues on
> equilibration when i run in CUDA the error is as follows
>
>
> *****************
>
>
> ERROR: Calculation halted. Periodic box dimensions have changed too much
> from their initial values.
>
> Your system density has likely 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.
>
> ************************
>
>
> SO I have ro run the equilibration in CPU based sander.MPI and I can run
> the MD using CUDA will this fix the issues or what I should do
>
>
> thank you
>
> On Wed, Sep 2, 2015 at 3:09 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> Hi Lara,
>>
>> Can you send me - directly to me and NOT to the list - the following file
>> please:
>>
>> $AMBERHOME/src/pmemd/src/mdin_ctrl_dat.F90
>>
>> Thanks,
>>
>> All the best
>> Ross
>>
>>> On Sep 2, 2015, at 12:04 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>>>
>>> Hi Lara,
>>>
>>> I think something is VERY wrong with your AMBER installation here. What
>> version of AMBER are you using, do you know what patches were applied and
>> how it was compiled?
>>>
>>> Do the test cases pass after installation?
>>>
>>> The default for nrespa should be 1.0 and so if it is not in your mdin
>> file it should never be defaulting to 2.0 unless something was very messed
>> up in your installation.
>>>
>>> All the best
>>> Ross
>>>
>>>> On Sep 2, 2015, at 11:51 AM, Lara rajam <lara.4884.gmail.com> wrote:
>>>>
>>>> Dear Amber !
>>>>
>>>> I have changed the input as below
>>>>
>>>> Heating up the system equilibration stage 1
>>>>
>>>> &cntrl
>>>>
>>>> nstlim=200000, dt=0.001, ntx=1, irest=0, ntpr=1000, ntwr=1000,
>> ntwx=1000,
>>>>
>>>>
>>>> tempi =0.0, temp0=300.0, ntt=1, tautp=2.0,
>>>>
>>>>
>>>> ntb=1, ntp=0,
>>>>
>>>>
>>>> ntc=2, ntf=2,
>>>>
>>>>
>>>> ntr=1,
>>>>
>>>> /
>>>>
>>>> Group input for restrained atoms
>>>>
>>>> 50.0
>>>>
>>>> RES 1 148
>>>>
>>>> END
>>>>
>>>> END
>>>>
>>>>
>>>>
>>>> still I get the error !
>>>>
>>>> the output by default takes the nrespa=2
>>>>
>>>> as below
>>>>
>>>>
>>>> Heating up the system equilibration stage 1
>>>>
>>>> &cntrl
>>>>
>>>> nstlim=100000, dt=0.002, ntx=1, irest=0, ntpr=1000, ntwr=500, ntwx=500,
>>>>
>>>>
>>>> tempi =0.0, temp0=300.0, ntt=1, tautp=2.0,
>>>>
>>>>
>>>> ntb=1, ntp=0,
>>>>
>>>>
>>>> ntc=2, ntf=2,
>>>>
>>>>
>>>> nrespa=2, ntr=1,
>>>>
>>>> /
>>>>
>>>> Group input for restrained atoms
>>>>
>>>> 50.0
>>>>
>>>> RES 1 148
>>>>
>>>> END
>>>>
>>>> END
>>>>
>>>>
>>>>
>>>> CUDA (GPU): Implementation does not support nrespa.
>>>>
>>>> Require nrespa == 1.
>>>>
>>>>
>>>> Input errors occurred. Terminating execution.
>>>>
>>>>
>>>>
>>>> still it get killed
>>>>
>>>>
>>>>
>>>> On Wed, Sep 2, 2015 at 2:40 PM, David A Case <david.case.rutgers.edu>
>> wrote:
>>>>
>>>>> On Wed, Sep 02, 2015, Lara rajam wrote:
>>>>>
>>>>>> CUDA (GPU): Implementation does not support nrespa.
>>>>>> Require nrespa == 1.
>>>>>
>>>>> Just leave out any reference to nrespa in your &cntrl namelist.
>>>>>
>>>>> ...hope this works....dac
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 02 2015 - 16:00:04 PDT
