From: Azadeh Alavi (azade.alavi_at_gmail.com)
Date: Sun Dec 20 2015 - 14:30:07 CST
Dear Jeff
Thank you very much for your reply. Does this way of restarting the
simulations have any significant effect on the results? My simulations
are in the equilibration stage. For your suggestion to make the xsc
file, all the parameters except the a,b and c are zero. Wouldn't they
make any problem?
Thank you again.
Best regards,
Azadeh
On 12/20/15, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> 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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