Re: [gmx-users] g_tune_pme restart

On Fri, Aug 24, 2012 at 12:23 PM, Albert wrote: > Dear: > >I use g_tune_pme for MD production but it clashed before the job > finished since it is over cluster walltime limitation. I get the > following information from perf.out: > > mpirun -np 144 mdrun -npme -1 -s tuned.tpr -v -o md.trr -c m

Re: [gmx-users] KALP15-DPPC Tutorial

On 8/24/12 10:48 AM, Shima Arasteh wrote: Hi, I am doing the simulation of kalp15 in DPPC following the Justin's tutorial. In the " 2. Pack the lipids around the protein "step, to get the correct area per lipid, I enter these commands: #perl inflategro.pl system.gro 4 DPPC 14 system_in

[gmx-users] g_tune_pme restart

Dear: I use g_tune_pme for MD production but it clashed before the job finished since it is over cluster walltime limitation. I get the following information from perf.out: mpirun -np 144 mdrun -npme -1 -s tuned.tpr -v -o md.trr -c md.gro -e md.edr -g md.log I am just wondering, is it co

[gmx-users] Electrostatics and van Der Waals in Gromacs

Dear Gromacs users, I am trying to get a full understanding of how the energy of electrostatics and VDW interactions are calculated in Gromacs, but I am not sure I have the right picture in mind. Could someone let me know if the procedure below is correct? So, let's say I have a PDB file, an

Re: [gmx-users] deltaG from PMF

Thanks for this! Steven On Fri, Aug 24, 2012 at 3:26 PM, Thomas Schlesier wrote: > As a first step, i would shift all curves so, that the energy of the minium > is for all plots at the same (aribarity) value. The minimum should be the > point which has sampled the best. If you shift then all val

Re: [gmx-users] Re: g_rms and g_rmsdist on initial structure

Because it uses the atom index, which is most likely NOT the same as your processed file will not contain certain hydrogens, which are present in A.pdb. 24 aug 2012 kl. 16.33 skrev Hsinlin: > Thank you for your reply. > I checked the coordinates of all C-alpha atoms between two .pdb files. > The

Re: [gmx-users] BAR / g_bar problems

Hi, David- Perhaps we can work with you to compare the internal g_bar implementation with our external BAR and MBAR implementation run from the .dhdl.xvg data output in 4.6. It would probably be easier to run these calculations after the optimization updates are added in the next few days(?), but

[gmx-users] KALP15-DPPC Tutorial

Hi, I am doing the simulation of kalp15 in DPPC following the Justin's tutorial. In the " 2. Pack the lipids around the protein "step, to get the correct area per lipid, I enter these commands:    #perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat Updating the .top fil

[gmx-users] Re: g_rms and g_rmsdist on initial structure

Thank you for your reply. I checked the coordinates of all C-alpha atoms between two .pdb files. They are exactly the same. So I don't understand why g_rms(g_rmsdist) selecting group C-alpha give me high values. Sincerely yours, Hsin-Lin Erik Marklund wrote > > Hi, > > Since gromos-forcefields

[gmx-users] Re: g_rms and g_rmsdist on initial structure

-- View this message in context: http://gromacs.5086.n6.nabble.com/g-rms-and-g-rmsdist-on-initial-structure-tp5000492p5000495.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

[gmx-users] deltaG from PMF

As a first step, i would shift all curves so, that the energy of the minium is for all plots at the same (aribarity) value. The minimum should be the point which has sampled the best. If you shift then all values, it should be easier to spot differences between the plots. And probably make the

Re: [gmx-users] g_rms and g_rmsdist on initial structure

Hi, Since gromos-forcefields are not strictly all-atom forcefields, there might be a mismatch between atoms in the two structures. Best, Erik 24 aug 2012 kl. 15.35 skrev Hsin-Lin Chiang: > Hi, > > For example, I have a A.pdb as a initial structure file. > And I just used pdb2gmx on it to gen

[gmx-users] g_rms and g_rmsdist on initial structure

Hi, For example, I have a A.pdb as a initial structure file. And I just used pdb2gmx on it to generate another B.pdb file with GROMOS96 43a1 as its force filed. Then I select C-alpha atoms to calculate RMSD. echo 3 | g_rms -f B.pdb -s A.pdb I suppose the RMSD value should be 0, but the value is

[gmx-users] CHARMM and FEP calculations

Hi I asked a similar question a year ago about implementing CMAP in FEP calculations for gromacs 4.5.4. At the time I could not get the simulation to run with CMAP as it came up with: Fatal error: > Function type CMAP Dih. not implemented in ip_pert Helpfully, Mark suggested a modification to t

[gmx-users] BAR / g_bar problems

Hi, we have terrible problems to get reasonable results from BAR free energy calculations. We basically follow Justin's tutorial for solvation of methanol, ethanol, diethyl-ether and neopentane in water using OPLS but get very strange results. The free energy curves are here: http://folding.

Re: [gmx-users] deltaG from PMF

I did g_wham calculation as you suggested for: 10-30 ns 30-50 ns 10-50 ns In some cases of PMF curves the drift is 0.3 kcal/mol but in some cases it is over 1.5 kcal/mol so huge drifts. In terms of huge drifts what would you suggest ? Steven On Tue, Aug 21, 2012 at 5:48 PM, Justin Lemkul wrote:

[gmx-users] Re: equilibrium stage runs for too long

Dear Justin, I just tried running it using one node with 12 cores, and it's been completed successfully within a short time! Yes you are right, the system is under reparation and this probably causes those problems. I'm really grateful for your and Vitaly's help. Thank you very much!!! Clare

Re: [gmx-users] Re: equilibrium stage runs for too long

On 8/24/12 6:01 AM, Clare wrote: Dear Vitaly, Thank you so much for your suggestion!! I've run the simultion using one core as you suggested, and I can see two outputs on step 0 and step 100 now ( shown on the bottom), but it still took a while to only generate these two outputs. Maybe it is i

[gmx-users] Re: equilibrium stage runs for too long

Dear Vitaly, Thank you so much for your suggestion!! I've run the simultion using one core as you suggested, and I can see two outputs on step 0 and step 100 now ( shown on the bottom), but it still took a while to only generate these two outputs. Maybe it is indeed the problem of scaling as menti

[gmx-users] what's the difference between gen_seed and ld_seed?

Am 23.08.2012 23:11, schrieb gmx-users-requ...@gromacs.org: hello : > >I am a little bit confused about the difference between gen_seed and >ld_seed. I checked the manual, it is said: > >gen_seed >used to initialize random generator for random velocities, when gen_seed >is set to -1, the seed

[gmx-users] Gromacs-4.5.5 on GPU : Floating point exception

Gromacs-4.5.5 is built on GPU with OpenMM-4.1.1 binary package. But the standard gromacs gpu benchmark - dhfr failed with "Floating point exception". The benchmark name is : dhfr/GPU/dhfr-impl-1nm.bench Error Output: Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision) W