Re: saving coordinates as a PDB file after minimization in NAMD

From: Richard Law (rlaw_at_hanyou.llnl.gov)
Date: Tue Oct 25 2005 - 16:14:18 CDT

It's in the log file. Unless you're not creating one!

When you run namd2 do a re-direct:

namd2 something.in > something.log

On Tue, 25 Oct 2005, Richard Wood wrote:

> Thank you for that tip.
>
> Now, how do I get NAMD to write out the text from a
> dynamics run, as I wish to know which frame in a
> trajectory is the lowest in energy.
>
> Richard
>
> --- Richard Law <rlaw_at_hanyou.llnl.gov> wrote:
>
>>
>> If your .coor is in binary then you have
>> binaryoutput set to "yes". You
>> need to change that. (to "no".)
>>
>> Rich.
>>
>>
>> On Tue, 25 Oct 2005, Richard Wood wrote:
>>
>>> Hi all,
>>>
>>> How does on save the resulting coordinates of a
>> NAMD
>>> minimization in a format to do dynamics?
>>>
>>> I have a starting PDB and I want to run 1000 steps
>> of
>>> minimization, save it to a second PDB file and
>> then
>>> run dynamics.
>>>
>>> It says in the NAMD manual to use:
>>>
>>> "outputname < output PDB file >
>>>
>>> Acceptable Values: UNIX filename prefix
>>>
>>> Description: At the end of every simulation, NAMD
>>> writes two PDB files, one containing
>>> the final coordinates and another containing the
>> final
>>> velocities of all atoms in the simulation.
>>> This option specifies the file prefix for these
>> two
>>> files. The position coordinates will be saved
>>> to a file named as this prefix with .coor
>> appended.
>>> The velocities will be saved to a file named
>>> as this prefix with .vel appended. For example, if
>> the
>>> prefix specified using this option was
>>> /tmp/output, then the two files would be
>>> /tmp/output.coor and /tmp/output.vel."
>>>
>>> However, .coor files are binary files.
>>>
>>> So how do I obtain the coordinates?
>>>
>>> Richard
>>>
>>>
>>>
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