[gmx-users] problem regarding removal of water from final simulation system.

[Dallas B. Warren]

Two ways:

 

1 - turn them off with the visualisation software you are using, only
display the protein and lipid

2 - use editconf and the appropriate index groups

 

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of nitu sharma
Sent: Thursday, 11 June 2009 3:19 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] problem regarding removal of water from final
simulation system.

 

Dear all 

 I have done successfully simulation of membrane protein , but after
that to visualise my final model clearly I have to remove water
molecules from my system (protein+lipid+water).

But  I have no Idea about the which command I should use to do this even
it doesn't mentioned in justin,s tutorial also to make final pdb after
simulation.

So can anyone suggest me  how to remove water form my final simulation
system to make final pdb of only protein and lipid molecule?

If anyone can help me I willbe really thankful for him/her.

Nitu Sharma.
Jawaherlal Nehru University
New Delhi , India.

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