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

[James Lord]

Hi Justin,
Thanks, apparently I am doing some silly mistakes as I checked for another
system I have and ended up to the same problem. I am sending all the files
to your personal email and then if the problem is solved I will send a post
with description of the problem and the solution to the mailing list. Is
that fine with you?
Cheers
James

On Sun, Oct 19, 2014 at 4:26 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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