Re: [gmx-users] mdrun cpt

2013-10-29 Thread Mark Abraham
On Oct 29, 2013 1:26 AM, "Pavan Ghatty" wrote: > > Now /afterok/ might not work since technically the job is killed due to > walltime limits - making it not ok. Hence use -maxh! Mark > So I suppose /afterany/ is a better > option. But I do appreciate your warning about spamming the queue and ye

Re: [gmx-users] virtual sites

2013-10-29 Thread Justin Lemkul
On 10/29/13 2:21 AM, Neha Gandhi wrote: Dear Users, I have a system consisting of peptides and a linear carbohydrate. Initially I tried to simulate these peptides using virtual sites and it worked. I can use pdb2gmx for building virtual sites on protein whereas I have an itp file for the carbo

[gmx-users] Constant-Force Pulling of Ubiquitin

2013-10-29 Thread Weiwei Tao
Hi GMX Users, I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin and it's a implicit model. My mdp file for pulling is shown as following. integrator = md dt = 0.001; ps ! nsteps = 50 ; total 500 ps. nstxout

[gmx-users] pbc problem

2013-10-29 Thread shahab shariati
Dear Mark Very thanks for your reply > To make this clear, center the trajectory on the water and watch the > time evolution in some visualization program. I did your suggestion (center the trajectory on the water). Again, drug molecule is in region (1)in some frames and is in region (4) in othe

[gmx-users] Constant-Force Pulling of Ubiquitin

2013-10-29 Thread Vivian
Hi GMX Users, I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin and it's a implicit model. My mdp file for pulling is shown as following. integrator = md dt = 0.001; ps ! nsteps = 50 ; total 500 ps. nstxout

Re: [gmx-users] pbc problem

2013-10-29 Thread Mark Abraham
On Tue, Oct 29, 2013 at 5:02 PM, shahab shariati wrote: > Dear Mark > > Very thanks for your reply > > > To make this clear, center the trajectory on the water and watch the > > time evolution in some visualization program. > > I did your suggestion (center the trajectory on the water). Again, dru

Re: [gmx-users] Constant-Force Pulling of Ubiquitin

2013-10-29 Thread XAvier Periole
You want to switch to sd instead of md. > On Oct 29, 2013, at 17:43, Vivian wrote: > > Hi GMX Users, > > I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin > and it's a implicit model. My mdp file for pulling is shown as following. > > integrator = md >

[gmx-users] g_rotacf error

2013-10-29 Thread Tiago Gomes
Hello gromacs users, I´m currently tring to calculate S2 order parameters for comparison with nmr data and other simulations. When i try the command for the NH vector: g_rotacf -s ../protein.tpr -d -P 2 -n nh.ndx -f ../protein_fit.xtc -w -noaver It gives me the only half of the residues (NH vecto

Re: [gmx-users] virtual sites

2013-10-29 Thread Roland Schulz
On Tue, Oct 29, 2013 at 2:21 AM, Neha Gandhi wrote: > Dear Users, > > I have a system consisting of peptides and a linear carbohydrate. > Initially I tried to simulate these peptides using virtual sites and > it worked. I can use pdb2gmx for building virtual sites on protein > whereas I have an i

Aw: Re: [gmx-users] Constant-Force Pulling of Ubiquitin

2013-10-29 Thread lloyd riggs
I dont know how well v-rescale works with pulling.  It could be after removing some restraints it still had not reached a good equilibrium (ie let it run a while/nanosecound or 5, before pulling it), or maybe generating velocities on start causes more caos than the proteins or system can handle, s

[gmx-users] hydrogen bond analysis

2013-10-29 Thread larif sofiene
Greeting I'm working on a MD of a ligand-protein complex during 40 ns i want to analyses ligand-protein interaction hydrogen bonds My first question : Should i analyses a minimized frame from clustering of the trajectory or should i analyses hydrogen bond occupancy over trajectory ? My

Re: [gmx-users] pbc problem

2013-10-29 Thread Justin Lemkul
On 10/29/13 12:02 PM, shahab shariati wrote: Dear Mark Very thanks for your reply To make this clear, center the trajectory on the water and watch the time evolution in some visualization program. I did your suggestion (center the trajectory on the water). Again, drug molecule is in region

Re: [gmx-users] g_rotacf error

2013-10-29 Thread Justin Lemkul
On 10/29/13 4:02 PM, Tiago Gomes wrote: Hello gromacs users, I´m currently tring to calculate S2 order parameters for comparison with nmr data and other simulations. When i try the command for the NH vector: g_rotacf -s ../protein.tpr -d -P 2 -n nh.ndx -f ../protein_fit.xtc -w -noaver It give

Re: [gmx-users] hydrogen bond analysis

2013-10-29 Thread Justin Lemkul
On 10/29/13 5:46 PM, larif sofiene wrote: Greeting I'm working on a MD of a ligand-protein complex during 40 ns i want to analyses ligand-protein interaction hydrogen bonds My first question : Should i analyses a minimized frame from clustering of the trajectory or should i analyse

[gmx-users] Simulate partially hydrolized polyacrylamide in solutions

2013-10-29 Thread qugm...@126.com
Hi,everyone, I'm a newcomer, i want to simulate partially hydrolized polyacrylamide in solutions,please give me some suggestions,how to build the polymer pdb structure and how to opitimize the structure, thank U! Qu Guangmiao qugm...@126.com-- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] RE: Gibbs Energy Calculation and charges

2013-10-29 Thread Dallas Warren
Just want this to make another pass, just in case those in the know missed it. Using couple-intrmol = yes the resulting dH/dl plot actually looks like that at lamba = 1 it is actually equal to couple-intramol = no with lambda = 0. Should that be the case? Catch ya, Dr. Dallas Warren Drug Deliv

Re: [gmx-users] RE: Gibbs Energy Calculation and charges

2013-10-29 Thread Michael Shirts
I think the grammar got a little garbled there, so I'm not sure quite what you are claiming. One important thing to remember; 1-4 interactions are treated as bonded interactions right now FOR COUPLE intramol (not for lambda dependence of the potential energy function), so whether couple-intramol i