Re: [AMBER] Ptraj for diffusion coefficient of water

From: Ganesh Kamath <gkamath9173.gmail.com>
Date: Sat, 22 Jan 2011 15:32:33 -0500

Hi,

  I am using NVT ensemble for 901 molecules of water, and langevin
Temperature control at 298 K.
The NVT results in a density of 0.998 g/cm^. I am storing the snapshots at
1ps interval. I was initially using NpT ensemble but decided that NVT would
be a better control after reading the Nilson paper for water models
comparison.

Could you please provide some suggestions.

Also this is the way I prepared the water.top file for TIP3P model. Am I
doing something wrong. Please let me known

loadamberparams frcmod.tip3p
loadoff tip3p.lib
reac = loadpdb water.pdb
charge reac
savepdb reac mix.pdb
setbox reac vdw
saveamberparm reac wat.top wat.crd
savepdb reac watnew.pdb

thanks for all the help.

ganesh


*My tip3p.lib file *


!!index array str
 "TIP"
!entry.TIP.unit.atoms table str name str type int typex int resx int
flags int seq int elmnt dbl chg
 "H1" "HT" 0 1 131075 1 1 0.417000
 "H2" "HT" 0 1 131075 2 1 0.417000
 "OH2" "OT" 0 1 131075 3 8 -0.834000
!entry.TIP.unit.atomspertinfo table str pname str ptype int ptypex int
pelmnt dbl pchg
 "H1" "HT" 0 -1 0.0
 "H2" "HT" 0 -1 0.0
 "OH2" "OT" 0 -1 0.0
!entry.TIP.unit.boundbox array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.TIP.unit.childsequence single int
 2
!entry.TIP.unit.connect array int
 0
 0
!entry.TIP.unit.connectivity table int atom1x int atom2x int flags
 1 3 17
 2 3 17
!entry.TIP.unit.hierarchy table str abovetype int abovex str belowtype
int belowx
 "U" 0 "R" 1
 "R" 1 "A" 1
 "R" 1 "A" 2
 "R" 1 "A" 3
!entry.TIP.unit.name single str
 ""
!entry.TIP.unit.positions table dbl x dbl y dbl z
 0.210000 0.853000 0.0
 1.491000 1.758000 0.0
 1.171000 0.853000 0.0
!entry.TIP.unit.residueconnect table int c1x int c2x int c3x int c4x
int c5x int c6x
 0 0 0 0 0 0
!entry.TIP.unit.residues table str name int seq int childseq int
startatomx str restype int imagingx
 "TIP" 1 4 1 "?" 0
!entry.TIP.unit.residuesPdbSequenceNumber array int
 1
!entry.TIP.unit.solventcap array dbl
 -1.000000
 0.0
 0.0
 0.0
 0.0
!entry.TIP.unit.velocities table dbl x dbl y dbl z
 0.0 0.0 0.0
 0.0 0.0 0.0
 0.0 0.0 0.0






On Sat, Jan 22, 2011 at 10:03 AM, case <case.biomaps.rutgers.edu> wrote:

> On Fri, Jan 21, 2011, Ganesh Kamath wrote:
> >
> > 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.
>
> Was any thermostat or barostat used for the NAMD simulation? That would
> make the simulation suspect for calculating time-dependent properties.
>
> Also, were the snapshots in namd indeed saved at 1 ps intervals?
>
> ...regards...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Sat Jan 22 2011 - 13:00:02 PST
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