Maybe you can try, just ONCE, to write the temperature trajectory from
the remd trajectory, and see if that mdcrd file behaves 'correctly' ?
Adrian
On 9/13/10 1:09 PM, Carlos Simmerling wrote:
> Amber11 is the latest for sander.
>
> so in the ptraj output it says that there are 20,000 frames, and has a dot
> for each? it reads all without error?
> and you are using the same prmtop to read the output trajectory? is it
> correct? meaning have you visualized the output trajectory using something
> like VMD, and the frames are correct but there are too few? what it is that
> tells you there are too few frames?
> thanks, these will help troubleshoot your problem.
>
> On Mon, Sep 13, 2010 at 7:04 AM, Jorgen Simonsen<jorgen589.gmail.com>wrote:
>
>> sure - I am using amber10 and ambertools 1.4 which should be the lastest.
>>
>> On Mon, Sep 13, 2010 at 12:41 PM, Carlos Simmerling<
>> carlos.simmerling.gmail.com> wrote:
>>
>>> it's not possible to help unless you specify which version of sander and
>>> which version of ptraj/ambertools.
>>>
>>> On Mon, Sep 13, 2010 at 6:19 AM, Jorgen Simonsen<jorgen589.gmail.com
>>>> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I have performed a remd with a 250.000 number of exchange trials during
>>> the
>>>> simulation every 0.5 ps. I have set ntwx=5.000 so I would expect 25.000
>>>> structures in my simulation but after processing the data using the
>>> script
>>>> to extract the coordinates at different temperatures I get
>>>>
>>>> #!/bin/csh
>>>>
>>>> ptraj l_dermorphin.prmtop<< EOF
>>>> trajin remd.mdcrd.001 remdtraj remdtrajtemp 300.0
>>>> trajout remd.300K.mdcrd nobox
>>>>
>>>> distance d1 out dist.300K.dat :1.CA :7.CA
>>>>
>>>> go
>>>> EOF
>>>> which reads all the output files
>>>>
>>>> Processing AMBER REMD trajectory (new format) files remd.mdcrd.001 ->
>>>> remd.mdcrd.010
>>>>
>>>> I only get 19999 structures - when I grep *REMD*' in the mdcrd.001 file
>> I
>>>> get 25.000 lines with REMD as expected. I do not know where my mistake
>> is
>>>> any help appreciated
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--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
Senior Editor. Journal of Physical Chemistry.
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Mon Sep 13 2010 - 04:30:06 PDT
