[gmx-users] GROMOS atp file

[Justin Lemkul]

On 8/15/15 9:51 AM, faride badalkhani wrote:
> But all the nonbonded parameters for these Hydrogens are zero while they
> are polar and they should be considered
>

This is the convention of the force field.  Polar groups are dominated by 
electrostatics.  The van der Waals interactions are parametrized with the 
assumption that the H do not need LJ terms; the heavy atoms dominate the 
interaction.  This is just the way this particular force field works.  Look at 
the well depth and radii of HC - it's essentially non-existent, as well.

-Justin

> On Sat, Aug 15, 2015 at 4:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 8/15/15 4:42 AM, faride badalkhani wrote:
>>
>>> Dear all,
>>>
>>> I am having a question about Hydrogens in GROMOS FF. There are two
>>> Hysrogens in .atp file of GROMOS FF as follows:
>>>
>>>      HC   1.00800 ;     hydrogen bound to carbon
>>>         H   1.00800 ;     hydrogen not bound to carbon
>>>
>>> and all the nonbonded parameters for H are considered zero, but what about
>>> polar Hydrogens that are bounded to elements other than C (for example H
>>> in
>>> amino or amid groups)? How should I treat with these polar hydrogens?
>>>
>>>
>> That's what atom type H is - "hydrogen *not* bound to carbon."
>>
>> -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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
==================================================

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

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