Re: problem with solvating a structure

From: João Ribeiro (
Date: Tue Feb 26 2019 - 14:48:12 CST

Dear Hadi,

For future reference, questions related to VMD and its plugins should be
posted in the mailing list.

Now, answering your question, VMD prints a lot of useful information in
the terminal window. Would it be possible for you to post the messages
print to the terminal after you executed the solvated command?



On Tue, Feb 26, 2019 at 2:35 PM Hadi Rahmaninejad <>

> Hello Dear NAMD users,
> I am using psfgen in VMD TkConsole in order to solvate a silica structure
> containing mostly Si and O atoms with water. The command I am using are:
> "solvate silica.psf silica.pdb -t 10"
> However, the result is a pdb file in which the coordinate of most of Si
> and O is "zero" (0.000). and so the vmd shows a weird structure of one Si
> connected to few oxygen and Hydrogen surrounded by water molecules. I
> highly appreciate if anybody can help me with this.
> Thank you in advance,
> Hadi

João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
+1 (217) 3005851

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