Re: [gmx-users] simulation using tabulated dihedral potentials.

Dear Justin and Mark, Thanks for the reply. I have regenerated the potentials for the bonded and non-bonded part. I observe the similar behavior as previous. Keeping dihedral switched off, the simulation proceeds. Taking in account the dihedral, the simulation shows the similar behavior. Now, I

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

my script is #!/bin/bash trjconv -s 10nsnvt.tpr -f 10nsnvt.trr -o noPBC.xtc -pbc none -ur compact -center -n index.ndx << EOF 2 0 EOF trjconv -s 10nsnvt.tpr -f noPBC.xtc -o fit.xtc -fit rot+trans -n index.ndx << EOF 2 0 EOF g_spatial -f fit.xtc -s 10nsnvt.tpr -n index.ndx << EOF 6 7 EOF g_spa

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

To help you, I need to see the exact commands that you used. Best is if you can put it all in a script, run the script to be sure that you see the problem, and then copy and paste the script back to this list. Failing that, copy and paste your commands and tell me what your command-line input wa

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

my script is #!/bin/bash trjconv -s 10nsnvt.tpr -f 10nsnvt.trr -o noPBC.xtc -pbc none -ur compact -center -n index.ndx << EOF 2 0 EOF trjconv -s 10nsnvt.tpr -f noPBC.xtc -o fit.xtc -fit rot+trans -n index.ndx << EOF 2 0 EOF g_spatial -f fit.xtc -s 10nsnvt.tpr -n index.ndx << EOF 6 7 EOF g_sp

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

my script is #!/bin/bash trjconv -s 10nsnvt.tpr -f 10nsnvt.trr -o noPBC.xtc -pbc none -ur compact -center -n index.ndx << EOF 2 0 EOF trjconv -s 10nsnvt.tpr -f noPBC.xtc -o fit.xtc -fit rot+trans -n index.ndx << EOF 2 0 EOF g_spatial -f fit.xtc -s 10nsnvt.tpr -n index.ndx << EOF 6 7 EOF g_sp

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

I meen after g_spatial calculation done. visualisation problem coming. molecule and SDF surface are overlapping somewhat . why? is this wrong result -- View this message in context: http://gromacs.5086.x6.nabble.com/g-spatial-mergin

Re: [gmx-users] g_spatial: merging solvent ond solute:::need some distance

I meen after g_spatial calculation done. visualisation problem coming. molecule and SDF surface are overlapping somewhat . why? is this wrong result -- View this message in context: http://gromacs.5086.x6.nabble.com/g-spatial-mergi

Re: [gmx-users] Potential energy calculations

Yes I know what you mean, however when your looking over a unit cell and trying to define a single molecule in the solvent (even as represented by the entire solvent makup), does it properly alighn the energy based on the averidged "zero" point.  I ask, not knowing, but playing with this (single s

[gmx-users] g_spatial: merging solvent ond solute:::need some distance

g_spatial Use make_ndx to create a group containing the atoms around which you want the SDF 2. trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none 3. trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans 4. run g_spatial on the .xtc output of step #3. 5. Load grid.cube into VMD and

Re: [gmx-users] question regarding free energy calculations

Hello Dr. Justin, So, the option "couple-intramol = yes" can be used to selectively turn off vdw and coulombic interactions of only few atoms from the rest of the molecule using a B state topology in Gromacs, as mentioned by Asaf. On Thu, Dec 26, 2013 at 6:37 PM, Justin Lemkul wrote: > > > O

Re: [gmx-users] question regarding free energy calculations

On 12/25/13, 4:55 AM, Asaf Farhi wrote: Dear all Hi. We have a question regarding the implementation of free energy calculations in Gromacs that we have been trying for long time to decipher. The question is the following: When transforming molecule A to B if the non bonded interactions are

Re: [gmx-users] Potential energy calculations

On 12/26/13, 5:30 AM, lloyd riggs wrote: Zero it--> If you plot a potential energy value strait from the simulation it will be something like point a) -7000 point b) -7050 across a single simulation. Thus you have to find a beginning point and subtract it across the run. Additionally, fluctua

[gmx-users] Parrinello-Rahman barostat: temperature and potential energy depend on tau_p

Dear GMX-Users, I am simulating pure supercritical CO2 fluid in NPT ensemble. Reference temperature is 308.15K. I use “sd” (Langevin dynamics) to control temperature with tau_t = 2ps. After 100 ps of equilibration in NPT with Berendsen thermostat, I run production simulation of 10 ns with Parrine

Re: [gmx-users] Potential energy calculations

  Also, if your not doing a diffusion type thing where half or a portion of one side of the box is DMSO and the other water, like say 100% DMSO but averidging, such as a random equilibrated solution of small molecules, the energy system will be sinusoidal, thus any energy plots vs. time will fluct

Re: [gmx-users] Potential energy calculations

Zero it--> If you plot a potential energy value strait from the simulation it will be something like point a) -7000 point b) -7050 across a single simulation.  Thus you have to find a beginning point and subtract it across the run.  Additionally, fluctuations may dictate 10 or so runs to determin