[gmx-users] Analysis

[Justin Lemkul]

On 5/20/16 9:16 AM, SOUVIK MONDAL wrote:
> I have converted dcd to xtc file and calculated rmsd. But in the output file the x coloumn (time) comes out be 0.0 all the time. How can I get proper time output?
>

Assign proper times with trjconv -t0 and -timestep options.

-Justin

> ----- Original Message -----
> From: jkrieger at mrc-lmb.cam.ac.uk
> To: gmx-users at gromacs.org
> Sent: Friday, May 20, 2016 4:39:14 PM
> Subject: Re: [gmx-users] Analysis
>
> Hi,
>
> If you can't save a GROMACS compatible xtc from vmd then I suggest using
> the mdconvert tool from mdtraj. It can convert between most commonly used
> md trajectory formats and have used it for both CHARMM dcd to
> GROMACS-compatible xtc and GROMACS xtc to a dcd that is readable by ProDy
> with no problems.
>
> Best wishes
> James
>
>> Hi,
>>
>> How to analyze in gromacs 4.5.7 from the  dcd file? I have vmd installed
>> in my computer.
>>
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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

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