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

[Justin Lemkul]

On 10/20/16 9:39 AM, Chapman, Christopher W. wrote:
> Hi,
>
> Thank you for your helpful comments and suggestions. Per your recommendations, I tried running my simulation with the original parameter set and configuration file, and the forces behave as one would expect. I tried re-generating the configuration file, however, and the simulation breaks down. I apparently created a correct configuration file once, and cannot recreate it.
>
> From what I can tell, since I'm using the TIP4P/2005f model, I cannot use Gromacs' built in solvate command because the .gro file it calls is based on the TIP4P model, which has slightly different values for the bond lengths and angles (though I may be wrong about not being able to use solvate). Because of this, I used my aforementioned script and just set the parameter values to their defaults given by the TIP4P/2005f model. The script generates the configuration file by creating an individual water molecule, randomly rotating it, and placing it in the box. This process is repeated until the box is full. Each molecule is offset from each other molecule by a set amount so that there is no overlap between any two water molecules. Each molecule is also checked to confirm that the rotations didn't alter the bond lengths, bond angles, and to ensure that all of the atoms lie in the same plane (there's no reason why the rotation should change these, but I figured I'd check just to
>  be safe). Is this an appropriate way to create the configuration file 'by hand'?
>

Just use the existing tip4p.gro and minimize it using the new topology.  Then 
you'll know immediately if the new topology is sensible, without complications 
of possible bad configurations.

-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 Justin Lemkul
> Sent: Tuesday, October 18, 2016 18:46
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] TIP4P/2005f parameter modification in Gromacs 5.1.2
>
>
>
> 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
>
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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

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