[gmx-users] Steered MD in gromacs

[Justin Lemkul]

On 9/3/13 3:10 PM, Gianluca Interlandi wrote:
> Also, why in vacuo? At least turn on an implicit solvent model.
>

I can think of reasons to study molecular interactions in vacuo via pulling. 
Why is solvent (explicit or implicit) an absolute requirement?

-Justin

> On Tue, 3 Sep 2013, Justin Lemkul wrote:
>
>>
>>
>> On 9/3/13 11:22 AM, hanna pdb wrote:
>>>
>>>
>>>
>>> Dear all,
>>>
>>> I am just starting MD simulations and wanted to see how to perform steered
>>> molecular dynamics in gromacs . Most papers and tutorials that I found were
>>> done in NAMD. Can anyone recommend examples that were done in gromacs?  In my
>>> case the tutorial " Pull Code and Umbrella Sampling" on the gromacs website
>>> seems not applicable. I "simply" want to see how to perform an in vacuo
>>> simulation by pulling.
>>>
>>
>> Indeed, my tutorial will go beyond what you want, but I don't see how it's not
>> applicable.  There is discussion of how to use all (or at least most) of the
>> pull settings and produce a SMD trajectory as part of the protocol.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>
>> ==================================================
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>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca at u.washington.edu
>                      +1 (206) 685 4435
>                      http://artemide.bioeng.washington.edu/
>
> Research Scientist at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
>                      http://healthynaturalbaby.org
> -----------------------------------------------------

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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