[gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2

[Justin Lemkul]

On 10/18/16 12:20 PM, Chapman, Christopher W. wrote:
> Hi Mark,
>
> Yes, my implementation does work for standard parameter values.
>

I agree with Mark.  You likely have a bad parameter set, and mdrun is telling 
you it is crashing.  Compute the forces in that trajectory and likely you will 
see where some bad behavior is emerging.  Force fields can be delicate, so what 
may seem like some small change can actually have profound consequences for 
stability.

-Justin

> Thanks,
>
> Chris
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Mark Abraham
> Sent: Tuesday, October 18, 2016 11:55
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2
>
> Hi,
>
> This looks like one manifestation of "the model physics is broken, and so is the resulting simulation system." Does your implementation behave for standard parameter values?
>
> Mark
>
> On Tue, Oct 18, 2016 at 5:34 PM Chapman, Christopher W. <chapmancw at ornl.gov>
> wrote:
>
>> Hello all,
>>
>> I am trying to model TIP4P/2005f water using Gromacs 5.1.2.
>> Specifically, I'm trying to show how modifying the parameters of the
>> TIP4P/2005f model changes the density of states. I wrote a small
>> script to randomly vary the parameters and write out the .gro and .top
>> files. When I tried running my molecular dynamics run, however, I got the following message:
>>
>>
>> A list of missing interactions:
>>                Morse of    686 missing      1
>>
>> Molecule type 'WAT'
>> the first 10 missing interactions, except for exclusions:
>>                Morse atoms    1    3           global    69    71
>>
>> Fatal error:
>> 1 of the 1029 bonded interactions could not be calculated because some
>> atoms involved moved further apart than the multi-body cut-off
>> distance
>> (0.294303 nm) or the two-body cut-off distance (1 nm), see option
>> -rdd, for pairs and tabulated bonds also see option -ddcheck For more
>> information and tips for troubleshooting, please check the GROMACS
>> website
>>
>>
>> I'm trying to figure out if this error is because the random values
>> for the parameters I chose were bad values (I sample them from a
>> log-normal distribution with a mean of the defined values of the
>> TIP4P/2005f values and a variance of 1% of those values), or if my
>> script is writing out the .gro and .top files incorrectly, or some
>> other cause. Any help that could be provided would be greatly appreciated.
>>
>> Thank you,
>>
>> Chris
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================