Re: [gmx-users] About MD

2011-09-26 Thread Jussi Lehtola
On Mon, 26 Sep 2011 09:31:39 +0200 xiaojing gong wrote: > Hi, many thanks for your answer. > > >> Any dynamical simulation has a lowest-energy structure... whether > >> this > means anything is another question. > > I am just wondering whether the structures you find with MD determined > mainly

Re: [gmx-users] About MD

2011-09-26 Thread Mark Abraham
On 26/09/2011 6:25 PM, xiaojing gong wrote: Hi, many thanks. I am doing some simulation correlated with the growth, in experiments, there are two kinds of growth, one is driven by kinetics and other is by thermodynamics. To address this question, I think you need to seek a better description

Re: [gmx-users] About MD

2011-09-26 Thread xiaojing gong
Hi, many thanks. I am doing some simulation correlated with the growth, in experiments, there are two kinds of growth, one is driven by kinetics and other is by thermodynamics. So I just wonder to know by using MD simulations, the results I obtained is driven by kinetics or thermodynamics. Silly

Re: [gmx-users] About MD

2011-09-26 Thread Mark Abraham
On 26/09/2011 5:31 PM, xiaojing gong wrote: Hi, many thanks for your answer. >> Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. I am just wondering whether the structures you find with MD determined mainly by thermodynamics (i.e. th

Re: [gmx-users] About MD

2011-09-26 Thread xiaojing gong
Hi, many thanks for your answer. >> Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. I am just wondering whether the structures you find with MD determined mainly by thermodynamics (i.e. the lowest energy structures) or by kinetics (i.e.

Re: [gmx-users] About MD

2011-09-26 Thread Mark Abraham
On 26/09/2011 6:41 AM, xiaojing gong wrote: Dear all， A question about, in MD, in which situation you can obtain a structure with lowest energy. Any dynamical simulation has a lowest-energy structure... whether this means anything is another question. Can MD simulate the kinetics process, a

[gmx-users] About MD

2011-09-25 Thread xiaojing gong
Dear all， A question about, in MD, in which situation you can obtain a structure with lowest energy. Can MD simulate the kinetics process, and obtain a stuctrue with the lowest activation barriers? Typically, are the structures we find with MD determined mainly by thermodyn

Re: [gmx-users] about md simulation

2007-09-11 Thread TJ Piggot
Also see http://wiki.gromacs.org/index.php/Thermostats As you do not want to temperature couple the sodium ions independently Tom --On Tuesday, September 11, 2007 18:14:43 +1000 Mark Abraham <[EMAIL PROTECTED]> wrote: amri ta wrote: Dear colleagues, I am simulating a phosphorylated prote

Re: [gmx-users] about md simulation

2007-09-11 Thread chiradip chatterjee
Hi Amrita, I have faced similar problem.before MD run, try to minimize water box and protein seperately with both CG and SD, then put protein in the water box and minimize it again .., then go for MD run, I think after that you dont have any Lincs warning.. Chiradip --- amri ta <[EMAIL PROTEC

Re: [gmx-users] about md simulation

2007-09-11 Thread amri ta
Dear colleagues, I am simulating a phosphorylated protein embedded in waterbox. When I try running mdrun, I get a LINCS warning. Does this mean that I have go back to the CG-EM step and use the double precision libs? The md.log file reads: Initializing LINear Constraint Solver number of constr

Re: [gmx-users] about md simulation

2007-09-11 Thread Mark Abraham
amri ta wrote: Dear colleagues, I am simulating a phosphorylated protein embedded in waterbox. When I try running mdrun, I get a LINCS warning. Does this mean that I have go back to the CG-EM step and use the double precision libs? These should help. http://wiki.gromacs.org/index.php/Err

[gmx-users] about md simulation

2007-09-11 Thread amri ta
Dear colleagues, I am simulating a phosphorylated protein embedded in waterbox. When I try running mdrun, I get a LINCS warning. Does this mean that I have go back to the CG-EM step and use the double precision libs? The md.log file reads: ... Initializing LINear Constraint Solver number