Re: Run simulation in NAMD using files generated by CHARMM-GUI

From: Bjoern Olausson (
Date: Tue Jun 01 2010 - 03:22:25 CDT

On Tuesday 01 June 2010 07:09:27 Dai, Jian1 wrote:
> Hi, NAMD users:
> We're trying to run DPPC bilayer simulation.
> The 1st question: I basically followed the steps of membrane builder on
> CHARMM-GUI to get the psf file in X-PLOR format and the pdb file. However,
> when viewing the structure, the two hydrogen atoms of water molecules
> appear to be linked together. Checking the relevant psf file section
> indicates that there are bonds between these two hydrogens. Is this what's
> supposed to be? The two hydrogen atoms of water are not bonded together in
> membranes generated by the MEMBRANE plugin of VMD.
Regrading your Water with three bonds, since I can't check your files I can
only guess that it depends on the chosen water model (I guess TIP3). If it is
tip3 then this is normal:

1 WATA 1 TIP3 OH2 OT -0.834000 15.9994 0 0.00000 -0.301140E-02
2 WATA 1 TIP3 H1 HT 0.417000 1.00800 0 0.00000 -0.301140E-02
3 WATA 1 TIP3 H2 HT 0.417000 1.00800 0 0.00000 -0.301140E-02

3 !NBOND: bonds
1 2 1 3 2 3

> The 2nd question: I
> used scripts to extract only the DPPC bilayer, i.e., no water molecules
> and then solvate the pure DPPC with the SOLVATE plugin of VMD.
What's the point of this step?

> When I
> tried to run the energy minimization, the simulation seems to be abnormal.
> The coordinates of atoms in the system hardly changes. The water molecules
> don't move. Can someone give us some suggestions? The configuration file,
> psf and pdb files are available at:
When you use a pre-equilibrated water box to build your system, why would you
expect the water molecules to move dramatically? They won't.
(I never used the SOLVATE plugin, but I guess VMD does what I would expect
from your description)

Please don't use rapidshare, use something more "serious" for sharing such
files. And please choose a service without waiting time and CAPTCHA stuff...

For us the University blocks rapidshare.


Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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