Re: solvate using Helmut Grubmuller's SOLVATE and then VMD, then how to minimize properly!

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Nov 11 2008 - 10:29:34 CST

It looks like there are two separate issues here.
First, the warnings in the log file indicate that you have some
incompatible definitions of atom types in several different parameter
files that you're using; you'll have to consider whether the files
you're using are all necessary and are compatible.

The NaNs during minimization generally mean that you have atoms with
non-unique coordinates or other unphysical starting conditions; you'll
need to carefully inspect your input coordinates to look for such things.

Best,
Peter

ydhuang2727 wrote:
> Hi, everyone !
> I use Helmut Grubmuller's SOLVATE
> (http://www.mpibpc.mpg.de/home/grubmueller/downloads/solvate/index.html)
> to generate a closely contoured solvent bubble around the solute, and
> then use VMD solvate to get the final cube。
> But when i run NAMD, some odd results in .log file generates as follows:
> Warning: DUPLICATE BOND ENTRY FOR ht-ht
> PREVIOUS VALUES k=0 x0=1.514
> USING VALUES k=0 x0=1.5139
> Warning: DUPLICATE vdW ENTRY FOR OT
> PREVIOUS VALUES sigma=3.1506 epsilon=0.1521 sigma14=3.1506
> epsilon14=0.1521
> USING VALUES sigma=2.8509 epsilon=0.1591 sigma14=2.8509 epsilon14=0.1591
> Warning: DUPLICATE vdW ENTRY FOR HT
> PREVIOUS VALUES sigma=0.4 epsilon=0.046 sigma14=0.4 epsilon14=0.046
> USING VALUES sigma=1.4254 epsilon=0.0498 sigma14=1.4254 epsilon14=0.0498
> Warning: DUPLICATE vdW ENTRY FOR CA
> PREVIOUS VALUES sigma=3.5501 epsilon=0.07 sigma14=3.5501 epsilon14=0.07
> USING VALUES sigma=3.517 epsilon=0.01 sigma14=3.517 epsilon14=0.01
> Warning: DUPLICATE vdW ENTRY FOR FE
> PREVIOUS VALUES sigma=1.1582 epsilon=1e-04 sigma14=1.1582 epsilon14=1e-04
> USING VALUES sigma=2.27 epsilon=0.01 sigma14=2.27 epsilon14=0.01
> Warning: DUPLICATE vdW ENTRY FOR ZN
> PREVIOUS VALUES sigma=1.9422 epsilon=0.25 sigma14=1.9422 epsilon14=0.25
> USING VALUES sigma=2.484 epsilon=0.01 sigma14=2.484 epsilon14=0.01
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> INITIAL STEP: 1e-06
> GRADIENT TOLERANCE: nan
> BRACKET: 0 nan nan nan nan
> RESTARTING CONJUGATE GRADIENT ALGORITHM
> INITIAL STEP: 5e-07
> GRADIENT TOLERANCE: nan
> BRACKET: 0 nan nan nan nan
> RESTARTING CONJUGATE GRADIENT ALGORITHM
> INITIAL STEP: 2.5e-07
> GRADIENT TOLERANCE: nan
> BRACKET: 0 nan nan nan nan
> NEW SEARCH DIRECTION
> INITIAL STEP: 1.25e-07
> GRADIENT TOLERANCE: nan
> BRACKET: 0 nan nan nan nan
> NEW SEARCH DIRECTION
> thanks very much!
> Dong
>
>
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