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

, since position restraints can only be applied per [moleculetype]. -Justin On Wed, Oct 31, 2012 at 3:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/12 3:55 PM, Alex Marshall wrote: Chris, is that for freeze groups or position restraints? I will assume Chris was referring

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

. 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 jalem...@vt.edu wrote: On 10/31/12 3:55 PM, Alex Marshall wrote: Chris, is that for freeze groups or position restraints? I

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

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 amars...@uwo.ca wrote: Justin: I'll try using position restraints instead

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

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 amarsh59 at uwo.ca wrote: Justin: I'll try using position restraints instead of freezing the water in the tube. Thanks for the tip. Bogdan: I

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

. I'll check the manual again though. Thanks. On Thu, Oct 25, 2012 at 10:43 AM, Bogdan Costescu bcoste...@gmail.comwrote: On Thu, Oct 25, 2012 at 3:59 PM, Alex Marshall amars...@uwo.ca wrote: Thanks Justin. I identified the offending waters using vmd (adding 1 to resID and atom number since vmd

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

24, 2012 at 9:22 PM, Justin Lemkul jalem...@vt.edu 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 using freeze groups at all times. I'm

[gmx-users] Freeze group atoms changing position

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/gmx-users

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

://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/Mailing_Lists -- Alex Marshall M.Sc. Candidate Department

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

for 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] Re: Measuring hydrogen bonding in a specific region

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-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages

Re: [gmx-users] Velocities in trjconv 4.5.5

/Support/Mailing_Lists -- Alex Marshall M.Sc. Candidate Department of Applied Mathematics The University of Western Ontario -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support

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 mark.abra...@anu.edu.auwrote: 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 were

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

), 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 University

[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

Re: [gmx-users] Dimensionless units question

= 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 amars...@uwo.ca wrote: Hi all, I'm trying to calculate the force on one particle and the total electrostatic energy of my system, which

Re: [gmx-users] Dimensionless units question

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, Alex Marshall amars...@uwo.ca wrote: Hi Amit, So if I understand you

[gmx-users] Slab Ewald test

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 search