[gmx-users] trjconv and -pbc

[vijaya subramanian]

-pbc atom

Date: Fri, 28 Oct 2011 06:34:28 +0200
Subject: Re: [gmx-users] trjconv and -pbc
From: tsjerkw at gmail.com
To: gmx-users at gromacs.org

Hi Lina,
Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump
Hope it helps,
Tsjerk
On Oct 28, 2011 6:27 AM, "lina" <lina.lastname at gmail.com> wrote:

On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Lina,
>
> Make su...I used the initial mdrun .tpr. After checking the generated pdb (total

51 frames), the first 28/29 frames both are together, but later are

separated. (the intra_fit also not work as expected).



So I think at beginning the reference initial ones are together.



This .xtc were trjcat together, first 200ns and then extend to 500ns,

the .pdb generated used dt 10ns.

>

> Cheers,

Am I wrong in some places? Actually for other trajectories I had no

problem (use the same way of handling it).



Thanks,

>
> Tsjerk
>
> On Oct 27, 2011 11:47 AM, "lina" <lina.lastname at gmail.com> wrote:
>
> Hi,
>
> I have ...

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