[gmx-users] Forces are large - How to track down the culprit

[Steffen Wolf]

Hi Shay,
sorry for the late comment - let me guess, you compiled Gromacs in
double precision? :)
Greetings
Steffen

> < Is this reproducible?
> Yes. I've taken the same simulation and had it re-run and got the same error
> at the exact same frame (frame 693, which is timeframe 6930).
>
> <You could try to fork off a tpr file using tpbconv -f -e -s -o just 
> <before this happens and rerun it.
> I did something similar to what you suggest before posting here:
> Oddly enough the Warning did not occur: I ran the simulation up to 6000ps
> and then continued the simulation to another 4000ps and the simulation ran
> correctly and without any problems.
>
> < It can also be combined by input parameters, e.g. too large time step, 
> <too infrequent neighborsearching etc., use of cutoffs.
> If no other suggestions I'll try working that angle too, since a lot of my
> simulations are running with very similar mdp parameters without problems.
>
> Thanks again for your prompt reply,
> -Shay
>
>
>
> Shay Amram wrote:
>   
>> Of course. I'm using version 3.3.3 of GROMACS. 
>> -Shay
>>
>> -----Original Message-----
>> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
>> On Behalf Of Mark Abraham
>> Sent: Tuesday, December 30, 2008 02:59 AM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] Forces are large - How to track down the culprit
>>
>> Shay Amram wrote:
>>     
>>> Greetings dear Gromacs users,
>>>
>>>  
>>>
>>> I have recently been simulating a POPG membrane* in water (SPC). Several 
>>> of my simulations after running well into the 10ns and 20ns are 
>>> sometimes getting a "Forces for atom X are large".  
>>>
>>> I'm rather unsure as to the cause of this situation. Moreover, as far as 
>>> I can tell from viewing the simulation, the system _does NOT_ explode 
>>> (as may be suggested by wiki.gromacs and some previous answers to this 
>>> kind of situation). The rest of the simulation looks much as it did in 
>>> the beginning.
>>>
>>> I would be interested (and thankful!) to hear any of your opinions as to 
>>> why I'm getting this message (or how to catch the culprit), and more 
>>> importantly, how to prevent it from happening in the future.
>>>       
>> During this version-transitive period, it's always right to report the 
>> GROMACS version that you're using. It would normally be right to be 
>> using the most recent version (4.0.2) if encountering problems.
>>
>> Mark
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>
>
>   


-- 
Dipl.-Chem. Steffen Wolf
Fellow of the Ruhr-University Research School
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: swolf at bph.rub.de
Web: http://www.bph.rub.de