Re: [gmx-users] Freeze group atoms changing position

Just as an update, I ran the simulation using position restraints with force constants set to 1 for each atom in the restrained waters, and none jumped out of the nanotube. Thanks for the help! On Thu, Nov 1, 2012 at 5:01 PM, Justin Lemkul wrote: > > > On 11/1/12 4:56 PM, Alex

Re: [gmx-users] Freeze group atoms changing position

ng out of bounds. Is it actually possible to only apply position restraints to some molecules within a species and leave the rest alone? On Wed, Oct 31, 2012 at 3:57 PM, Justin Lemkul wrote: > > > On 10/31/12 3:55 PM, Alex Marshall wrote: > >> Chris, is that for freeze groups

Re: [gmx-users] Freeze group atoms changing position

hey're identified with the appropriate topology > file. Does this sound like it would work? Is there some other way that you > might do it? > > Thanks > > On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall wrote: > > > Justin: I'll try using position r

Re: [gmx-users] Freeze group atoms changing position

oms I want to freeze so that they're identified with the appropriate topology file. Does this sound like it would work? Is there some other way that you might do it? Thanks On Fri, Oct 26, 2012 at 5:18 PM, Alex Marshall wrote: > Justin: I'll try using position restraints instead of

Re: [gmx-users] Freeze group atoms changing position

me two waters have jumped. I'll check the manual again though. Thanks. On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu wrote: > On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall wrote: > > Thanks Justin. I identified the offending waters using vmd (adding 1 to > > resID and at

Re: [gmx-users] Freeze group atoms changing position

24, 2012 at 9:22 PM, Justin Lemkul wrote: > > > On 10/24/12 3:17 PM, Alex Marshall wrote: > >> Hi all, >> >> I'm simulating a system of two reservoirs connected by a carbon nanotube. >> The reservoir wall atoms and carbon nanotube atoms are held in place

[gmx-users] Freeze group atoms changing position

but after 20 ns two of the frozen water molecules have jumped outside of the nanotube into a supposedly inaccessible region. What could cause this? Should I be worried? -- Thanks, Alex Marshall M.Sc -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] How to create two parallel wall?

rch 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. > * Can't post? Read http://www.gromacs.org/Support/Mailin

Re: [gmx-users] Re: Measuring hydrogen bonding in a specific region

are allowed! > * 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. > * Can't post? Read http://ww

[gmx-users] Measuring hydrogen bonding in a specific region

each reservoir Is there any way I could automate/improve this process? I have ten of these simulations longer than 100 ns to analyze, and I just need more data points than I can crank out manually. Thanks. -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western

Re: [gmx-users] Velocities in trjconv 4.5.5

to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-use

Re: [gmx-users] can mdrun append output files without the proper .cpt?

Thanks Mark! On Tue, Jan 31, 2012 at 7:26 PM, Mark Abraham wrote: > On 28/01/2012 7:09 AM, Alex Marshall wrote: > > Hi all, > I was trying to extend my simulation but I used the wrong .tpr file when I > called mdrun_mpi. I didn't catch it in time and my checkpoint files wer

[gmx-users] can mdrun append output files without the proper .cpt?

imulations), but when I use mdrun_mpi -append with the extended .tpr file, new output files are generated anyway. Is there a way around this, or will I just have to use trjcat or something once the new run has finished? Thanks. -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The

Re: [gmx-users] Dimensionless units question

ribution then LJ parameters should also be > correct and for that you should switch to standard gromacs units. > > Also why do you need to use gmx.ff, seems to me that you already have the > parameters (ie the LJ parameters and charges) > > > On Fri, Jul 29, 2011 at 11:30 AM, A

Re: [gmx-users] Dimensionless units question

u set charge = 1 it is 1electronic > charge. I would suggest not to use the reduced units for LJ in this > scenario. > > Amit > > On Fri, Jul 29, 2011 at 8:05 AM, Alex Marshall wrote: > >> Hi all, >> >> I'm trying to calculate the force on one particle and t

[gmx-users] Dimensionless units question

Hi all, I'm trying to calculate the force on one particle and the total electrostatic energy of my system, which consists of a lattice of 25 evenly spaced charges in the xy plane and a single charge in the center above to preserve charge neutrality. The reference values I have been given are in di

[gmx-users] Slab Ewald test

0 0 ; qtot 0 23 H 12 CHR H3 23 1 1 H 0 0 ; qtot 0 24 H 12 CHR H6 24 -1 1 H 0 0 ; qtot 0 25 H 13 CHR H3 25 1 1 H 0 0 ; qtot 0 26 H 13 CHR H6 26 -1 1 H 0 0 ; qtot 0 Thanks, Alex Marshall -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please