[gmx-users] Steered MD in gromacs

[Gianluca Interlandi]

> 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.

I'm sure there are.

G

> 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
>
> ==================================================
> -- 
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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
-----------------------------------------------------