[gmx-users] Re: simulation of protein/water and phosphate ion

Dallas Warren Dallas.Warren at monash.edu
Wed Sep 28 05:10:14 CEST 2011

What is actually blowing up?  The protein or the phosphate ions?  Do the phosphate ions run OK by themselves in water?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
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 bharat gupta
Sent: Wednesday, 28 September 2011 12:48 PM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Re: simulation of protein/water and phosphate ion


I tried simulating the system again but this time with 2 phsophate ion and the charge of the system was neutralized by adding 6 sodium ions . After minimizing , I equilibrated for 500 ps but I got "LINCS" error around 300ps.  It's happening due to the addition of phosphate ions as I have simulated my protein in water earlier without any problem. During nvt quilibration the temperature coupling settings were for Protein and Non protein groups. Do I have to make groups for Protein and water_ion. Please comment??
On Tue, Sep 27, 2011 at 7:09 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:jalemkul at vt.edu>> wrote:

bharat gupta wrote:

I have tried simulating my protein (GFP) solvated with water molecules and 10 phosphate ions. During the md run step the system starts exploding after  500 ps. What could be the reason for this . I know this is happening due to the addition of phosphate ion but I need to study the binding of ions . So, what shall I do ??




Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080

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