[gmx-users] Van der waals interaction between nanotubes

Dear all, Hi I am new to gromacs. I want to calculate the Van der waals interaction between two capped CNT facing each other using the pairwise LJ potential.I haven't used gromacs already. Any know-how/procedures to do the requiste would be very helpful.Whether Any tutorials are available

Re: [gmx-users] scaling of replica exchange

Hi Valeria, > Dear all, > I am making some tests to start using replica exchange molecular dynamics > on my system in water. The setup is ok (i.e. one replica alone runs > correctly), but I am not able to parallelize the REMD. Details follow: > > - the test is on 8 temperatures, so 8 replicas > -

Re: [gmx-users] scaling of replica exchange

Hi Valeria, > Dear all, > I am making some tests to start using replica exchange molecular dynamics > on my system in water. The setup is ok (i.e. one replica alone runs > correctly), but I am not able to parallelize the REMD. Details follow: > > - the test is on 8 temperatures, so 8 replicas > -

Re: [gmx-users] scaling of replica exchange

On 02/23/11, Valeria Losasso wrote: > > Dear all, > I am making some tests to start using replica exchange molecular dynamics on > my system in water. The setup is ok (i.e. one replica alone runs correctly), > but I am not able to parallelize the REMD. Details follow: > > - the test is on 8

[gmx-users] scaling of replica exchange

Dear all, I am making some tests to start using replica exchange molecular dynamics on my system in water. The setup is ok (i.e. one replica alone runs correctly), but I am not able to parallelize the REMD. Details follow: - the test is on 8 temperatures, so 8 replicas - Gromacs version 4.5.3

[gmx-users] Re: Adding chromophore parameters to the charmm force field

Hi, I have obtained the chromophore parameters of the GFP for charmm force field but I am not able to find it out how to add it to the charmm FF file.. I have two files one is the topology file , which looks like this :- * 221 MASS13 CP2c 12.01100 C ! his CE1 carbon MASS14 NR2c

Re: [gmx-users] configure: error: cannot compute sizeof (off_t)

On 23/02/2011 3:35 PM, Justin Kat wrote: Im not quite sure if this is the right place to analyze, but a bit before the part in the config.log where it states the error of "cannot compuete sizeof (off_t)", there is this: configure:25048: checking size of off_t configure:25053: /usr/local/bin/

[gmx-users] configure: error: cannot compute sizeof (off_t)

Im not quite sure if this is the right place to analyze, but a bit before the part in the config.log where it states the error of "cannot compuete sizeof (off_t)", there is this: configure:25048: checking size of off_t configure:25053: /usr/local/bin/mpicc -o conftest -O3 -fomit-frame-pointer -f

Re: [gmx-users] Can g_wham support using different temperature for different windows?

Sorry, why do you think the PMF should be asymmetric? I pulled my peptide from d=9nm (above the membrane) to d=-3nm (below the membrane) and I did windowed umbrella sampling in the range of d=-1.05nm to d=9nm. At least the PMF should be symmetric with respect of the bilayer center in the r

[gmx-users] Re:gmx-users Digest, Vol 82, Issue 168

Hi all, If anyone have a script that amb2gmx_dihe.pl provide by Guillem Portella,could you send me a copy? Thanks very much!-- 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/Mail

Re: [gmx-users] Re: Differences in rmsd with different force field

bharat gupta wrote: Since the paper that I am following says that for that protein (GFP) 1ns simulation is enough as other people carried out 10ns for the same protein and rmsd follows the same pattern which is being shown by that 1ns simulation .. When were those studies published? With m

Re: [gmx-users] Re: Differences in rmsd with different force field

Since the paper that I am following says that for that protein (GFP) 1ns simulation is enough as other people carried out 10ns for the same protein and rmsd follows the same pattern which is being shown by that 1ns simulation .. So I decided to do a 3ns simulation the RMSD that I got was same

Re: [gmx-users] Re: Differences in rmsd with different force field

bharat gupta wrote: Hi I did a simulation of 3 ns with OPLS AA 2001 Force Field for a protein of 230 aa and also I carried out a simulation of 10ns for the same protein but with different force field (Amber 2006) . I obtained the rmsd of the trajectories of both simulation , which I found t

[gmx-users] Re: Differences in rmsd with different force field

Hi I did a simulation of 3 ns with OPLS AA 2001 Force Field for a protein of 230 aa and also I carried out a simulation of 10ns for the same protein but with different force field (Amber 2006) . I obtained the rmsd of the trajectories of both simulation , which I found to be different ?? i.e. 3ns

Re: [gmx-users] Can g_wham support using different temperature for different windows?

Jianguo Li wrote: Thank you, Justin. Actually I did windowed umbrella simulations from d=-1.05nm to d=9nm. Since I think there is no problem in the region out of the membrane, so I only show the configurations within the membrane. My objective is to access the free energy barrier of the pept

Re: [gmx-users] Can g_wham support using different temperature for different windows?

Thank you for the the useful information, XAvier. My peptide is highly positively charged, 18 AA with +12 charges. Other of my group members told me their NMR experiment in water indicates the peptide conformation is very dynamics. Actually I also did peptide refolding using REMD in water, and

Re: [gmx-users] Can g_wham support using different temperature for different windows?

Thank you, Justin. Actually I did windowed umbrella simulations from d=-1.05nm to d=9nm. Since I think there is no problem in the region out of the membrane, so I only show the configurations within the membrane. My objective is to access the free energy barrier of the peptide translocate the ne

Re: [gmx-users] index file for interaction energies

Nick wrote: One last question! 1- So what are the 12 energy terms I get by passing index file onto step 2 below? I ignored rerun! what does rerun does? I don't know what 12 terms you're referring to. You'll get A-A, A-B, and B-B short-range nonbonded terms, the exact enumeration of wh

Re: [gmx-users] index file for interaction energies

One last question! 1- So what are the 12 energy terms I get by passing index file onto step 2 below? I ignored rerun! what does rerun does? 2- So I dont have to include index file in mdrun initially..In brief what I need is: step 1 grompp .(no index) step 2 mdrun -s old.tpr

Re: [gmx-users] index file for interaction energies

Nick wrote: Dear Justin, Thanks for your reply and Sorry for asking naive questions... 1- I am looking at all possible interaction energies between components A and B. that is A-A AB and BB. So interaction between single chains is not what I want. With this I think my initial approach was

Re: [gmx-users] index file for interaction energies

Dear Justin, Thanks for your reply and Sorry for asking naive questions... 1- I am looking at all possible interaction energies between components A and B. that is A-A AB and BB. So interaction between single chains is not what I want. With this I think my initial approach was right. That is putt

Re: [gmx-users] index file for interaction energies

Nick wrote: Dear experts, 1- I am trying to get interaction energies between solute (3 chains A) and solvent 50 molecules B. In the index file I created two groups: one for all atoms of [A] and and [B] for all solvent molecules. and by setting A and B as energy groups in mdp file I am getti

[gmx-users] index file for interaction energies

Dear experts, 1- I am trying to get interaction energies between solute (3 chains A) and solvent 50 molecules B. In the index file I created two groups: one for all atoms of [A] and and [B] for all solvent molecules. and by setting A and B as energy groups in mdp file I am getting break down as A-

[gmx-users] Re: problems with randoms seeds

ok, problem solved... used same .tpr file all the time should stop working for today :) greetings thomas On 02/22/2011 08:49 PM, Thomas Schlesier wrote: hi all, i'm trying out GROMACS 4.5.3 i'm simulating (sd-integrator) a small rna hairpin in vacuum, without pbc for 100ps. System has about 380

[gmx-users] problems with randoms seeds

hi all, i'm trying out GROMACS 4.5.3 i'm simulating (sd-integrator) a small rna hairpin in vacuum, without pbc for 100ps. System has about 380 atoms. If i do the simulation a second time (grompp + mdrun) i get identical results. first i had only *gen_seed = -1* but latter i set also *ld_seed = -

[gmx-users] test on g_density

Hi all. I've noticed an unexpected behaviour using g_density. I have a trajectory (with time step 2) and it is split into two subsets (using trjconv) with, lets say, even and odd steps respectively. According the the algorithm I expected that the density obtained with the original traject

[gmx-users] Dielectric constant for alkanes based on shell polarizable model

Dear Gromacs users, I really hope someone could give me some advise on my following problem.  I am simulating liquid bulk hexane using a shell (or Drude oscillator) model that incorporates the electronic polarization in GROMACS 4.5.3.  To do this, I use the force field parameters from the CHARMM d

Re: [gmx-users] Can g_wham support using different temperature for different windows?

A few notes: - the original method (Kumar-JCC-1992) that inspired wham was actually developed to mix different temperature simulations. It is however not clear for the type of system you are simulating how much a 500K simulation would be useful to improve the sampling at 300 K or so. The reaso

Re: [gmx-users] Can g_wham support using different temperature for different windows?

Jianguo Li wrote: Thanks Justin and Chris and sorry for confusing interpretation. Let me make it more clear. My peptide is flexible Martini beads, and highly positively charged. My membrane is a mixture of negatively charged lipids (25%) and zitterionic lipids(75%). So there is strong electr

[gmx-users] ffamber03 RB dihedrals and amb2gmx.pl problem!

Hello all I obtained a top file after running the "amb2gmx.pl" script,but I feel some errors in this top file. The functype of the [dihedral] is 3 in this top file,but the [pairs] part aslo presence in it. And the manual is point that "with the Ryckaert-Bellemans potential the 1-4 interactions

Re: [gmx-users] %exist hydrogen bond

leila karami wrote: Dear Justin My simulation system contains protein, dna and water. I used your script already for obtaining %exist hydrogen bonds between protein and dna: #!/usr/bin/perl # # plot_hbmap.pl - plot the probability of finding a particular hydrogen bond # based on several inpu

Re: [gmx-users] Can g_wham support using different temperature for different windows?

Sorry I forgot to attach my mdp files. Here is the mdp file for pulling simulaition: - title= Martini cpp = /usr/bin/cpp define = -DPOSRES_LIP integrator = md ; start t