From: Abhishek TYAGI (
Date: Wed Mar 30 2016 - 04:14:05 CDT


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.



Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

From: <> on behalf of Stefano Guglielmo <>
Sent: Wednesday, March 30, 2016 6:48 AM
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_--