Re: [AMBER] Queastions Regarding Tutorial A11 NCSU Method

From: Γιώργος Λαμπρινίδης <>
Date: Tue, 9 Oct 2012 09:43:48 +0300


I have already downloaded the input files and i have run them without
problem. My question is, how from the restart file of phase 1 (MD implicit
solvent), you go to the input file of phase 2 (MD explicit model) without
losing velocities. Because as i mentioned, phase 2 starts with "irest =1,
ntx =5", which means there must be a missing part.


> On Mon, Oct 8, 2012 at 9:48 PM, "Γιώργος Λαμπρινίδης" <
>> wrote:
>> Dear users,
>> I was trying to run a simulation according to Tutorial A11 (Pyranose
>> ring
>> puckering)
>> When I finish the "finer" run using Implicit solvent i get a restart
>> file,
>> containing the final velocities. In order to create the explicit solvent
>> job i transform prmtop and inpcrd files to pdb and I use tleap to create
>> the solvated files and i export them. With this procedure I loose all
>> velocities, so when i try to run the "flooding" procedure using the mdin
>> file from the tutorial i get an error "no velocities found", because of
>> the "irest =1, ntx =5" command.
>> How can overcome this error? Propably i am missing something.
>> In the tutorial how from the restart file of implicit solvent someone
>> goes
>> to "flooding" using explicit water?
> The input and output files are bundled in a tarball included as a download
> at the top of the tutorial. I would suggest looking through this to try
> and find your answer (presumably these input files still work, though I
> doubt they've been tested recently).
> Unfortunately, the NCSU capabilities have rather fallen out of maintenance
> and widespread use, at least among the developers, so getting a more
> helpful response may take a long wait (if it comes at all). Your best
> friends in this case are likely the input files provided on the website
> and
> the manual.
> HTH,
> Jason
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list

Dr Giorgos Lamprinidis
Researcher & Laboratory Assistant Staff
Faculty of Pharmacy
University of Athens - Greece
tel: +30 2107274304
     +30 2107274824
fax: +30 2107274747
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Received on Tue Oct 09 2012 - 00:00:04 PDT
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