[AMBER] Ptraj for diffusion coefficient of water

From: Ganesh Kamath <gkamath9173.gmail.com>
Date: Fri, 21 Jan 2011 15:52:54 -0500

Hi AMBER folks,

I used NAMD to run a box of 901 molecules of water using TIP3P model. I used
tleap to generate a tip.top for 901 molecules
and using TIP3P model. I tried using ptraj to read the namd file using the
tip.top as parm file to compute the diffusion coefficient of
water at 298 K I get 3.01*10-5 cm2/sec. which is incorrect.
AT the moment I dont understand why I am getting the wrong number. Can
anyone please help me.

thanks,
ganesh


*********details*****************

[ganesh.willis water]$ ~/ptraj10 tip.top

  \-/
  -/- PTRAJ: a utility for processing trajectory files
  /-\
  \-/ Version: "AMBER 10.0 integrated" (2/15/2008)
  -/- Executable is: "/home/ganesh/ptraj10"
  /-\
  \-/ Residue labels:

 WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
 ...
 WAT

 PRMTOP does not contain %FLAG RADIUS_SET

PTRAJ: Processing input from "STDIN" ...
trajin equil3.dcd

PTRAJ: trajin equil3.dcd
  Checking coordinates: equil3.dcd
diffusion :1-901 1.0 average diffusion

PTRAJ: diffusion :1-901 1.0 average diffusion
Mask [:1-901] represents 2703 atoms
go
[No output trajectory specified (trajout)]

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 100 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File (equil3.dcd) is a CHARMM trajectory in big endian binary format
    with box information representing 100 sets
  NFILE = 100 ISTEP = 1000 NINTV = 1000 NSAVC = 100000 NSAVV
= 0
  NDEGF = 0 NFREA = 0 DELTA = 0.0205 QCRYS = 1 QDIM4
= 0
  VERNU = 24 NATREC= 2703 NFREAT = 2703
  Dumping the title:
REMARKS FILENAME=equil3.dcd CREATED BY
NAMD
REMARKS DATE: 01/21/11 CREATED BY USER:
jpotoff

NO OUTPUT COORDINATE FILE WAS SPECIFIED

ACTIONS
  1> DIFFUSION
      Only the average results will be dumped to diffusion_?.xmgr
      The time between frames in psec is 1.000.
      To calculated diffusion constants, calculate the slope of the lines(s)
      and multiply by 10.0/6.0; this will give units of 1x10**-5 cm**2/s
      The atoms in the calculation follow: * (All atoms are selected)


Processing CHARMM trajectory file equil3.dcd

Set 1 .................................................
Set 50 .................................................
Set 100

PTRAJ: Successfully read in 101 sets and processed 100 sets.
       Dumping accumulated results (if any)

[ganesh.willis water]$ xmgrace diffusion_r.xmgr &


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Received on Fri Jan 21 2011 - 13:00:03 PST
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