From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Tue Jul 28 2015 - 09:34:21 CDT
I am slightly surprised that NAMD did not create the restart files for you.
What did you set your restart frequency as?
On Tue, Jul 28, 2015 at 12:03 AM, Felipe Merino <
> Hi Daniela,
> If you don't have the velocities for the configuration that you want to
> restart from (either restart.vel or a velocity trajectory) then you have to
> go from scratch.
> On 28/07/15 02:21, Daniela Rivas wrote:
> Hi Chitrak,
> Thank you, but the problem is I can't find those restart files. It seems
> like I forgot to add that line on my conf file. So, I want to know if it's
> possible to retake my simulation just using the output.dcd file, that'd be
> the only way, otherwise I'll have to run my dynamics all over again :(
> 2015-07-27 14:29 GMT-03:00 Chitrak Gupta <chgupta_at_mix.wvu.edu>:
>> Hi Daniela,
>> Yes, you can. In fact it is fairly simple. NAMD should have created the
>> restart files, specifically, the *.res.coor, *.res.vel and *.res.xsc files
>> which contain, respectively, coordinates, velocities, and periodic box
>> information. When you restart your simulation, make sure you read these
>> files (the manual should explain how to do this). Remember to not specify a
>> temperature as this is already being read from the *.vel file (I am
>> assuming a constant temperature run. If that's not what you were doing,
>> refer to the manual on how to restart that). Also, if you want the steps to
>> be numbered from where it last crashed, use the "firsttimestep" option.
>> Hope this helps,
>> On Mon, Jul 27, 2015 at 11:32 AM, Daniela Rivas <dani.rivas.r_at_gmail.com>
>>> It's my first time using Namd and I don't know how to continue my
>>> interrupted molecular dynamics simulation (electricity went off during the
>>> weekend). I have my output.dcd and output.xst files and also have the log
>>> file, so I know where to start again, I just don't know how to do it.
>>> Is there a way I can retake the simulation from the last point saved
>>> in the output?
>>> I hope someone can help me :)
> Felipe Merino
> Max Planck Institute for Molecular Physiology
> Department of Structural Biochemistry
> Otto-Hahn-Str. 11
> 44227 Dortmund
> Phone: +49 231 133 2306
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