Re: [AMBER] Ptraj for diffusion coefficient of water

From: Sergio R Aragon <aragons.sfsu.edu>
Date: Fri, 21 Jan 2011 23:10:19 +0000

Hello Ganesh,

The attached paper by Case and coworkers discuss the computation of diffusion coefficients with different water models (emphasis is on rotational diffusion, but a sufficient discussion of the translational diffusion of water is given). You also need a sufficiently long trajectory. Bottom line - the TIP3P water model is not appropriate because it reproduces the viscosity of water poorly. Try some of the other models as discussed in the paper.

Cheers, Sergio

Sergio Aragon
Professor of Chemistry
SFSU

-----Original Message-----
From: Ganesh Kamath [mailto:gkamath9173.gmail.com]
Sent: Friday, January 21, 2011 12:53 PM
To: AMBER Mailing List
Subject: [AMBER] Ptraj for diffusion coefficient of water

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 - 15:30:05 PST
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