Hi Matej,
Thank you for relay.
Unfortunately, your variant
trajin ../4_/sm_md4.mdcrd 2000 4000
selects snapshots inside the 4_ directory.
In contrast, the problem is how to select
snapshot from the time interval that covers the
border between two directories 3_ and 4_ as I wrote
in my example.
The question is still open.
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il
________________________________________
From: Repic Matej <matej.repic.epfl.ch>
Sent: Thursday, September 10, 2015 12:58 PM
To: AMBER Mailing List
Subject: Re: [AMBER] cpptraj script for average 3D protein structure?
I think adding another line after the trajin 3_ would do the trick:
trajin ../4_/sm_md4.mdcrd 2000 4000
Best,
Matej
------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC LCBC
BCH 4108
CH - 1015 Lausanne
------------------------------------------------------
On 9/10/15, 10:23, "Michael Shokhen" <michael.shokhen.biu.ac.il> wrote:
>Dear Amber List users,
>
>
>I now how write a cpptraj script for the generation of average protein
>structure from
>
>MD simulation in one directory as for instance:
>
>
>cpptraj
>parm ../sm.prmtop
>trajin ../3_/sm_md3.mdcrd 1001 2000
>strip :WAT
>strip :Cl-
>rms first .C,CA,N
>average average.pdb PDB
>run
>
>
>Unfortunately, I don't know how to write a cpptraj script for time
>interval
>
>that covers the border between two sequential directories of continuous
>MD simulation like in the task described below.
>
>
>I have ran productive MD simulation of my protein
>
>in two sequential time intervals 20ns (2000 snapshots) in directory 3_,
>
>and then continuing simulation of 20ns (2000 snapshots) in directory 4_.
>
>As a result I have in total 40ns (4000 snapshots) MD simulation.
>
>I want to generate average 3D structure of my protein on the last 30 ns
>
>(3000 snapshots) time interval that includes a border between two
>sequential MD simulations.
>
>
>What should be a cpptraj script for this case?
>
>
>Thank you,
>
>Michael
>
>
>
>
>*****************************
>Michael Shokhen, PhD
>Associate Professor
>Department of Chemistry
>Bar Ilan University,
>Ramat Gan, 52900
>Israel
>email:
>shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b
>9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Sep 10 2015 - 03:30:04 PDT
