Re: nan (Not a number) error in meta-eABF simulation

From: Dhiman Ray (dray1_at_uci.edu)
Date: Sun Sep 01 2019 - 03:11:02 CDT

Dear Haohao,

Thank you for your suggestion. I will try NAMD 2.13.

Best regards,

Dhiman.
************************************
Dhiman Ray
Graduate Student
Prof. Ioan Andricioaei group
University of California, Irvine
Department of Chemistry
Irvine, CA

On Sat, Aug 31, 2019 at 11:18 PM Haohao Fu <fhh2626_at_gmail.com> wrote:

> Dear Dhiman,
>
> This is an interesting issue that I have never met. I suggest that you
> first try NAMD 2.13. If it does not work, you can send the input files to
> me and I will see what I can do.
>
> Best,
> Haohao
>
> Dhiman Ray <dray1_at_uci.edu> 于2019年9月1日周日 上午11:02写道:
>
>> Dear NAMD users,
>>
>> I am recently facing an issue with the meta-eABF calculations in the GPU
>> version of NAMD 2.12. For long simulations (>20 ns), the NAMD starts
>> printing -nan (Not a number) in its output (.log, .colvars.traj, .xsc etc.
>> files). *The simulation does not stop or it does not print any error
>> message*. I have tried with changing the parameters of eABF and
>> metadynamics, (and also timestep of dynamics) but that did not make any
>> difference. Also NAMD starts printing -nan at different times for different
>> runs. I have carefully checked that there is no rapid increase in energy or
>> force prior to the point when nan is being printed.
>>
>> I have performed much longer metadynamics and eABF simulations with the
>> same system without any issues. Surprisingly two of my meta-eABF
>> simulations went on till 200 ns and gave converged results while the rest
>> printed nan. This has become completely unpredictable. Also I cannot
>> restart the trajectories because the simulation does not stop and keeps on
>> replacing the .restart.xsc, .restart.vel, .restart.coor files with nan. So
>> I do not have any good restart file.
>>
>> I am following this paper for meta-eABF implementation in NAMD:
>> https://pubs.acs.org/doi/10.1021/acs.jpclett.8b01994
>>
>> Please suggest me how to overcome this problem.
>>
>> Thank you,
>>
>> Dhiman.
>> ************************************
>> Dhiman Ray
>> Graduate Student
>> Prof. Ioan Andricioaei group
>> University of California, Irvine
>> Department of Chemistry
>> Irvine, CA
>>
>>

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