VMD-L Mailing List

From: Abhishek TYAGI (atyagiaa_at_connect.ust.hk)
Date: Wed Mar 30 2016 - 04:14:05 CDT

Hi,

you may try following things:

1. Start vmd in text mode and using removewater script remove water/ions from big dcd file, it will remove water and ions from your dcd file and make new dcd file without water including new pdb and psf file without water.

# Remove the directories from a path, leaving only the file name.
proc trimPath {name} {
    set ind [string last "/" $name]
    return [string range $name [expr $ind+1] end]
}

# Remove water and silicon material from a dcd file.
proc removeWater {structPrefix dcd} {
    # Select the water or silicon material.
    set selText "(not water and not ion) and (not resname S1)"
    # Prefix to add to the output dcd files:
    set outPrefix "nw_";

    # Load the system.
    mol load psf $structPrefix.psf pdb $structPrefix.pdb
    set sel [atomselect top $selText]
    set dcdName [trimPath $dcd]
    set structName [trimPath $structPrefix]

    # Write the structure files for the resulting system.
    $sel writepsf nw_${structName}.psf
    $sel writepdb nw_${structName}.pdb

    # Load the trajectory.
    animate delete all
    mol addfile $dcd waitfor all
    set last [expr {[molinfo top get numframes]-1}]

    # Write the dcd files for the selection.
    animate write dcd "nw_$dcdName" beg 0 end $last waitfor all sel $sel top

    $sel delete
    mol delete top
}

2. You may use catdcd tool to make small dcd files, as required by you.

http://www.ks.uiuc.edu/Development/MDTools/catdcd/

Best

Abhi

Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Stefano Guglielmo <stefano.guglielmo_at_unito.it>
Sent: Wednesday, March 30, 2016 6:48 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: error loading dcd

Dear vmd users,

I am trying to load a dcd file of a molecular dynamic simulation, but after several frames (a little more than 5000) a runtime error occurred for microsoft visual c++ runtime library, which causes abnormal termination for vmd--_000_HK2PR0199MB060960C5330E6B8F916AAE24F6980HK2PR0199MB0609_--