Hi,
I am only using cis/trans, chirality restraints so far.
By the way, I think I solved the problem. It's because I am using 40
replicas, but one of my scripts only read up to rep 39, so there was a
problem. I change my script and everything is fine now.
Thanks,
Thanh
Quoting Carlos Simmerling <carlos.simmerling.gmail.com>:
> ok- you probably want to use extensive restraints during MD.
>
>
> On Wed, Jun 15, 2011 at 9:57 AM, <tdo.chem.ucsb.edu> wrote:
>
>> Hi Dr. Simmerling,
>>
>> Thank you. Yes I am aware of the issues you mentioned in the last
>> reply. I am interested in structures in vacuum, so we think high
>> temperatures are needed to explore different conformations.
>>
>> Thank you,
>>
>>
>>
>>
>>
>> Quoting Carlos Simmerling <carlos.simmerling.gmail.com>:
>>
>> > Dan Roe can probably answer about the error- but are you sure you want to
>> > run at 2100K? There are many, many things that can go wrong in
>> simulations
>> > at such a high T, and it's not clear that it's needed.
>> >
>> > just want to make sure you know what you're doing, if you are aware of
>> the
>> > issues then it's fine of course!
>> >
>> >
>> > On Wed, Jun 15, 2011 at 9:49 AM, <tdo.chem.ucsb.edu> wrote:
>> >
>> >> Hi,
>> >>
>> >> I am running REMD and use ptraj to extract trajectories from mdcrd
>> outputs.
>> >>
>> >> Here is the script
>> >>
>> >> trajin ./remd.00 remdtraj remdtrajtemp 300.0
>> >> trajout traj300K.dat pdb append
>> >>
>> >> It works fine until recently I get some messages:
>> >>
>> >> REMDTRAJ: Final repTemp value read= 1043.840000, set 302
>> >> Could not find target 300.000000 in any of the replica trajectories.
>> >> Check that all replica trajectory files were found and that
>> >> none of the trajectories are corrupted (e.g. missing a temperature).
>> >> ptrajProcessInputCoordinates(): Target replica temperature not found
>> >> in traj! 100%
>> >>
>> >>
>> >> PTRAJ: Successfully read in 301 sets and processed 301 sets.
>> >>
>> >>
>> >> It only happens to 2/5 of my simulations that I am running (5
>> >> different systems using identical method). It seems that ptraj can
>> >> only read 300/450 sets of trajectories. So I wonder if this happens
>> >> due to something wrong in my simulations, or ptraj itself.
>> >>
>> >> My simulation has max temp ~ 2100K, in vacuum.
>> >>
>> >>
>> >> Thanks,
>> >>
>> >>
>> >>
>> >> --
>> >> Thanh D. Do
>> >> Department of Chemistry & Biochemistry
>> >> University of California Santa Barbara
>> >> Santa Barbara, California, 93106
>> >>
>> >>
>> >>
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Thanh D. Do
>> Department of Chemistry & Biochemistry
>> University of California Santa Barbara
>> Santa Barbara, California, 93106
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanh D. Do
Department of Chemistry & Biochemistry
University of California Santa Barbara
Santa Barbara, California, 93106
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 15 2011 - 07:30:06 PDT
