Hello,
My work-around to the 0 velocity issue is to create a reimaged restart file from the last frame in the trajectory and then copying the velocities from the original restart to the new restart. This assumes ntwx and ntwr have the same value.
I will note though, that lately I've been running into restart files that don't have complete velocity information... This is when I have to restart with 0 velocities. I want to say this has only happened in amber 11 for me.
-Trevor
________________________________________
From: Arvind [bahuroopi.gmail.com]
Sent: Monday, September 20, 2010 3:51 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Error due to ***s in restart file
On Mon, Sep 20, 2010 at 2:44 AM, case <case.biomaps.rutgers.edu> wrote:
> On Mon, Sep 20, 2010, Arvind wrote:
>
>> The restart file generated using ptraj does not have ***s, but
>> after a point, all the coordinates come out as 0.0000000.
>
> The zeroes are (probalby) not coordinates but velocities. A trajectory file
> doesn't have any velocities, to ptraj uses zeroes as placeholders. You
> could proably use that restart file (with a non-zero value for tempi).
I do want it to continue from the previous velocities, so that is not an option.
> You probably want to set iwrap=1 to avoid having the same problem recur.
It will lead to a loss of any information on diffusion etc. But i
think i have no other choice, so i will go for that option.
Thanks for the inputs.
regards,
arvind
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Received on Tue Sep 21 2010 - 22:30:06 PDT
