[gmx-users] Steered MD in gromacs

[Gianluca Interlandi]

Also, why in vacuo? At least turn on an implicit solvent model.

Gianluca

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
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> 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
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