From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Sun Dec 20 2015 - 12:46:16 CST
Sorry, accidentally bumped the send button.
You can easily make a .coor file from the .dcd. Just load your trajectory
in VMD and do:
set all [atomselect top all]
$all writenamdbin blah.coor
You have to reinitialize the velocities using the "temperature" command in
NAMD. This is only a problem if you are studying flows or something.
If your system is orthonormal, you can generate the xsc like this:
set a [molinfo top get a]
set b [molinfo top get b]
set c [molinfo top get c]
set out [open blah.xsc w]
puts $out "# NAMD extended system configuration restart file"
puts $out "#\$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
s_x s_y s_z s_u s_v s_w"
puts $out [list 0 $a 0 0 0 $b 0 0 0 $c 0 0 0 0 0 0 0 0 0]
close $out
Jeff
–––––––––––––––––––––––––––––––––––———————
Jeffrey Comer, PhD
Assistant Professor
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
Phone: 785-532-6311
On Sun, Dec 20, 2015 at 12:06 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> You can easily make a .coor file from the .dcd.
>
> set all [atomselect top all]
> $all writenamdbin blah.psf
>
> The
>
>
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
>
> On Sun, Dec 20, 2015 at 3:02 AM, Azadeh Alavi <azade.alavi_at_gmail.com>
> wrote:
>
>>
>> Dear Namd users,
>>
>> Unfortunately, I have forgotten to use the "restratsave" command in my
>> configuration file and I want to restart from a few nanoseconds before my
>> last timestep. My simulations are in NPT ensemble. I would be grateful if
>> you could tell me how to get the restart files, especially the .xsc file,
>> from the dcd file I have or any other way possible.
>>
>> Thank you very much.
>>
>> Best regards,
>> Azadeh
>>
>
>
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