[gmx-users] Binding of a drug to a lipid bilayer using umbrella sampling method

[Khuong Truong Gia]

Dear Justin,

I got it. Thank you very much for your kindly reply.

Best regards,
Khuong

On Tue, Mar 29, 2016 at 6:56 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/28/16 9:02 PM, Khuong Truong Gia wrote:
>
>> Dear all,
>>
>> I am running umbrella sampling simulation about binding of a drug
>> (polymer)
>> to a lipid bilayer. Could you please suggest me how can I do
>> position-restraints the reference group (bilayer)? Do I need to restraint
>> all lipid molecules?
>>
>
> You should not have to apply position restraints to anything.
>
> As I read in the gromacs manual there is cylinder option for the
>> pull-geometry, but I am not sure this is suitable for my system or not?
>> Please give me some advice.
>>
>
> Yes, that is a good choice, as the example in the manual is almost
> identical to what you're doing.
>
> -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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