And where are these waters? Close to the phosphate ions? You really need to be asking more questions, looking at the trajectory file / frames when it blows up, and determining what is actually going on by yourself.
Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@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-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of bharat gupta Sent: Wednesday, 28 September 2011 1:30 PM To: Discussion list for GROMACS users Subject: [gmx-users] Re: simulation of protein/water and phosphate ion it's showing error that certain atoms cannot be settled and these atoms are of solvent molecules i.e. Water On Wednesday, September 28, 2011, Dallas Warren <dallas.war...@monash.edu<mailto:dallas.war...@monash.edu>> wrote: > 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.war...@monash.edu<mailto:dallas.war...@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-boun...@gromacs.org<mailto:gmx-users-boun...@gromacs.org> > [mailto:gmx-users-boun...@gromacs.org<mailto:gmx-users-boun...@gromacs.org>] > On Behalf Of bharat gupta > Sent: Wednesday, 28 September 2011 12:48 PM > To: jalem...@vt.edu<mailto:jalem...@vt.edu>; Discussion list for GROMACS users > Subject: Re: [gmx-users] Re: simulation of protein/water and phosphate ion > > > > Hi, > > 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 > <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: > > bharat gupta wrote: > > HI, > > 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 ?? > > > > http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu<http://vt.edu> | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org<mailto:gmx-users@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to > gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > Bharat > Ph.D. Candidate > Room No. : 7202A, 2nd Floor > Biomolecular Engineering Laboratory > Division of Chemical Engineering and Polymer Science > Pusan National University > Busan -609735 > South Korea > Lab phone no. - +82-51-510-3680, +82-51-583-8343 > > Mobile no. - 010-5818-3680 > E-mail : monu46...@yahoo.com<mailto:monu46...@yahoo.com> > > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com<mailto:monu46...@yahoo.com>
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