[gmx-users] Modify TIP4P to TIP4P-Ew

[Justin Lemkul]

On 11/22/14 11:27 AM, Cai wrote:
> Justin, thanks for your reply. I forgot to mention that I would like to use
> OPLS-AA force field together with TIP4P-Ew water in my protein-water
> simulation. Since TIP4P-Ew is not available in OPLS-AA force field, I still
> need to modify TIP4P to TIP4P-Ew. Could you give me some suggestions for
> doing this? Do have to touch the source code?
>

You just need to create a similar topology - all you should have to do is add 
new atom types and use the topology basically as-is.  There are no code 
modifications required to build a new topology.

-Justin

>
>
> On Sat, Nov 22, 2014 at 5:00 AM, <
> gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
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>>     1. Re: Modify TIP4P to TIP4P-Ew (Justin Lemkul)
>>
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>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 21 Nov 2014 16:48:14 -0500
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] Modify TIP4P to TIP4P-Ew
>> Message-ID: <546FB31E.1040808 at vt.edu>
>> Content-Type: text/plain; charset=utf-8; format=flowed
>>
>>
>>
>> On 11/21/14 4:41 PM, Cai wrote:
>>> Hi users,
>>>
>>> The re-parameterized TIP4P-Ew water model shows encouraging agreements
>> with
>>> experimental results. Since it is now not available in GROMACS, I have to
>>> modify the TIP4P water model to TIP4P-Ew according to this paper.
>>>
>>> (Horn et. al. (2004). Development of an improved four-site water model
>> for
>>> biomolecular simulations: TIP4P-Ew. *The Journal of Chemical Physics*,
>>> *120*(20),
>>> 9665?78).
>>>
>>> Q1:
>>> I know how to change the water parameters (angle, rOH, ...) in the
>> topology
>>> file (***.top/itp) and implement the Ewald-summation (coulombtype = PME).
>>> Is that all? It seems the paper also include correction for LJ by
>>> multiplying switching function, adding LJ tail, and correction for
>>> pressure, which are not easy to do in GROMACS. Any suggestions for doing
>>> these?
>>>
>>> Q2:
>>> Is it possible to do that without touching the source code?
>>>
>>
>> The TIP4P-Ew model is already available in all of the Amber force fields
>> provided with Gromacs.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> 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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>> End of gromacs.org_gmx-users Digest, Vol 127, Issue 118
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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

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