Re: reg: quenching NAMD trajectory

From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu Jun 06 2019 - 16:37:56 CDT

Hi Lara,

If I understand correctly, you want to post-process an existing DCD by
minimizing and then outputting the new coordinates as a DCD. I'm not sure
this is possible, but I can get you partly there using the coorfile and
output commands (which are documented, but not in great detail):

## normal system set up
coorfile open dcd <dcdfilename>
set nframes -1
while {![coorfile read]) {
    incr nframes
    minimize <number of steps>
    output <basename w/label dependent on $nframes>
}
coorfile close

output generates a set of .coor, .vel, and .xsc files with the basename as
the argument. That's a lot messier than a DCD both in terms of the number
of files and the extra data for velocities, but it's not so bad with good
bookkeeping. You can also delete unwanted files on-the-fly in the script.

HTH,
BKR

On Thu, Jun 6, 2019 at 3:49 PM Lara rajam <lara.4884_at_gmail.com> wrote:

> Dear NAMD users
> I would like to energy minimize each frame to 2000 steps and then write
> the final coordinates , This I want to do it for all the MD frames .
> Any informations will be useful Thank you
>
> On Thu, Jun 6, 2019 at 3:44 PM Pratik Narain Srivastava <
> pratik.narain_at_gmail.com> wrote:
>
>> If by quenching you mean decrease the number of frames then just load the
>> trajectory using the stride function. After loading your PDB and PSF files,
>> when you select you DCD, apply a stride value of total_frames/2000 in the
>> appropriate field to get 2000 frames loaded.
>>
>> On Fri, 7 Jun, 2019, 1:11 AM Lara rajam, <lara.4884_at_gmail.com> wrote:
>>
>>> Dear Namd Users
>>> I would like to quench the MD generated dcd files ( minimizing to 2000
>>> steps).
>>> Can any one let me know the possibilities of doing this
>>> thanks in advance
>>>
>>

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