Re: how to get the restart files from the dcd file?

From: Azadeh Alavi (azade.alavi_at_gmail.com)
Date: Mon Dec 21 2015 - 07:10:47 CST

Dear Jeff

Thank you again for your help. I did as you told me, but the simulation was
terminated with the constraint failure in rattle algorithm and atoms moving
too fast error which I presume is due to the use of temperature instead of
the .vel file. I would be thankful if you could also help me about it. I
reduced the timestep but it did not work.

Best regards,
Azadeh

On Mon, Dec 21, 2015 at 10:06 AM, Amitkumar Majhi <kumaramitmajhi_at_gmail.com>
wrote:

> sorry for inconvenience reply.
>
> On Mon, Dec 21, 2015 at 12:05 PM, Amitkumar Majhi <
> kumaramitmajhi_at_gmail.com> wrote:
>
>> sir I came to SERC, you were in meeting, one of your colleague informed
>> me. When shall I come there again?
>>
>> regards
>> Amit
>>
>> On Mon, Dec 21, 2015 at 2:00 AM, Azadeh Alavi <azade.alavi_at_gmail.com>
>> wrote:
>>
>>> 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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