VMD-L Mailing List

From: Bylund, Tatsiana (NIH/NIAID) [F] (tatsiana.bylund_at_nih.gov)
Date: Tue Mar 01 2016 - 10:32:54 CST

Thank you very much, Josh!

From: Josh Vermaas <vermaas2_at_illinois.edu<mailto:vermaas2_at_illinois.edu>>
Date: Tuesday, March 1, 2016 at 11:14 AM
To: "Bylund, Tatsiana (NIH/NIAID) [F]" <tatsiana.bylund_at_nih.gov<mailto:tatsiana.bylund_at_nih.gov>>
Cc: "vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>" <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>
Subject: Re: vmd-l: visualizing MDFF results with explicit solvent

Use atomselections to only show the part you are interested in. For instance, to get rid of water, the selection text "not water" will work. You can use the same selection to write out a dehydrated trajectory.
Josh

On Mar 1, 2016 7:34 AM, "Bylund, Tatsiana (NIH/NIAID) [F]" <tatsiana.bylund_at_nih.gov<mailto:tatsiana.bylund_at_nih.gov>> wrote:
Dear all,
I run simulations with explicit solvent. When I visualize them it's hard to see my molecule because of the solvent.
Can I get rid of the solvent in my dcd file or do something so that I actually see the molecule?

Thank you very much!

Best regards,
Tatsiana