[gmx-users] How to calculate protein-surface interaction energy

[Justin Lemkul]

On 10/18/14 9:55 AM, James Lord wrote:
> You are right it is the name of molecule type in .top, and thus no error
> upon executing grompp, so index group is constructed correctly right???

In theory, but if you're saying that at t=0, LJ-SR is not zero, something is 
weird.  Without access to your files, it's impossible to diagnose that any further.

-Justin

> rvdw=1 nm so should be fine. and for the last part I agree.
> Cheers
> James
>
> On Sun, Oct 19, 2014 at 2:34 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 10/18/14 9:30 AM, James Lord wrote:
>>
>>> Hi Justin,
>>>
>>> 1. Make sure your index groups are correctly constructed.
>>> Do I need to use make ndx? I thought just adding energygrps=protein
>>> surface
>>> at the end of .mdp is enough?
>>>
>>>
>> "Surface" isn't likely a default group (unless that's the name of the
>> [moleculetype]) and grompp should have raised a fatal error if the group
>> wasn't defined.
>>
>>   2. What does 5 nm correspond to?  A COM distance?  A minimum distance?  If
>>> the latter, then the LJ-SR energy should likely be zero, but if it's a COM
>>> distance, that's not necessarily the case.
>>> 5 nm is minimum distance
>>>
>>>
>> OK, in this case, the initial LJ-SR should be zero, provided that rvdw < 5.
>>
>>   3. Is your PE model united-atom or all-atom?  If the latter, you still
>>> have
>>> partial charges that will contribute to a negative Coul-SR (of course,
>>> this
>>> is something you can check very simply
>>> It is all atom
>>>
>>
>> Then you must have partial charges on the individual atoms and therefore
>> Coul-SR will be non-zero.
>>
>>
>> -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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-- 
==================================================

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

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