[gmx-users] regarding box volume

[Justin Lemkul]

On 8/29/15 9:37 AM, Johnny Lu wrote:
> I am new to simulation and haven't done any simulation for finding free
> energy. The following is my guess.
>
> How big are the molecules?
> If the box size is small then the concentration of the molecules is higher.
>
> May be the dissociation part is fine if:
> the hybrid can't see its mirror image (the intermolecular force between the
> hybrid and its mirror image is very weak).
> the partially dissociated hybrid can't see its mirror image.
>
> The rebinding part is fine if:
> Once the hybrid completely dissociated (AB --> A+B), both A and B have
> enough space such that A can't see B for a while.
>
> What do you want to know?
> If you want to know the free energy of the dissociation, may be the
> following tutorial can help:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/02_topology.html
> I guess that tutorial only require the hybrid can't see its mirror image.
>
> Might need thermodynamic cycle:
> http://openi.nlm.nih.gov/detailedresult.php?img=3203851_1741-7007-9-71-4&req=4
>

Binding free energy in this case should be calculated with umbrella 
sampling/PMF, not the alchemical methods above.  Those will never converge for 
large molecules, at least not in any practical amount of time.

-Justin

>
> On Sat, Aug 29, 2015 at 7:14 AM, soumadwip ghosh <soumadwipghosh at gmail.com>
> wrote:
>
>> Ignore the previous mail.
>>
>> Hi,
>>      please excuse me if my question appears very silly to you. I have a
>> hybrid of a Carbon nanotube and a polymer and I want to study the
>> unwrapping dynamics of the polymer in presence of a polymer binding agent.
>> I kept the hybrid inside a triclinic box and am doing simulations in
>> presence of that binder for 100 ns. The size of the box is around 277 nm3.
>> Is there a possibility that once the hybrid dissociates the polymer may not
>> have enough volume to go apart from the CNT and hence affecting the correct
>> dynamics picture? Should I perform such kind of simulations in a bigger
>> box? I might be missing out something very fundamental. Your help would be
>> appreciated.
>>
>> Sorry if I am asking for much.
>> --
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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

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