Re: [gmx-users] Initial velocity

Thanks so much for your support, The point is that, I have this mathematical theory on coarse grain simulation for which is supposed to resolve the potential existing between atoms suspended by an angle theta(like the triangle share for two atoms). To solve for the potential, the theta between

Re: [gmx-users] question about energygrps

Huyjin, If you look in your log file from the rerun you will see that when running using the GPU, energy groups are ignored or unused for energy reporting. Thus for this to work you need to run it on the CPUs. This is what I get in my output md.log when trying the same thing... NOTE: With

[gmx-users] Issue running gromacs in Cluster

Hello, I am trying to run 20 ns protein ligand simulation on cluster using following MD.MDP file ; 7.3.3 Run Control integrator = md; leap-frog integrator dt = 0.002 ; 2 fs nsteps = 500;

Re: [gmx-users] Issue running gromacs in Cluster

You may have created large files and thus got out of quota on the disc. Check your quota and consider reducing the frequency of saving coordinates. On May 13, 2013, at 9:46, Sainitin Donakonda saigr...@gmail.com wrote: Hello, I am trying to run 20 ns protein ligand simulation on cluster

Re: [gmx-users] Issue running gromacs in Cluster

On 13/05/2013 08:46, Sainitin Donakonda saigr...@gmail.com wrote: Hello, I am trying to run 20 ns protein ligand simulation on cluster using following MD.MDP file ; 7.3.3 Run Control integrator = md; leap-frog integrator dt = 0.002

[gmx-users] umbrella sampling

HI, I would like to compute an umbrella sampling simulation for o protein divided in two domain, with Center of mass pulling using as constraint between the two domains. And the constraint is applied instead of a harmonic potential I create a pull.mdp file with this option for the pull: title

Re: [gmx-users] Difference between g_rms and g_rmsdist

Thanks a lot for your answer. 2013/5/10 Justin Lemkul jalem...@vt.edu On 5/10/13 4:24 AM, Nawel Mele wrote: Hi, I am trying to understand what is the difference between g_rms and g_rmsdist commands. I have looked at the manual and all I can find is that: *g_rms*: The root mean square

Re: [gmx-users] Issue running gromacs in Cluster

Thank you very much for inputs but i forgot to mention in previous query i got one error ..with other protein ligand simulation i used same MD file saving 200 steps.. *Cannot write trajectory frame; maybe you are out of quota?* * * Whats the solution for this error ? is this same problem with

[gmx-users] Center of Mass (COM) spacing between protein and ligand

Respected Sir many many thanks for your reply to my last mail. I was able able to debug the error Here I have new set of queries.. How much COM spacing should i consider for my protein-ligand interactiom How much total distance I should move along z-axis/... and which all conf file should i take

[gmx-users] air-water-interface

Hi all, I am performing a simulation of protein at air/water interface. For create an air-water interface I just expand the box in the z direction. So,aAfter minimization we can noticed that water molecules moved out of bulk water in the z direction. Why you just need to expand the z-axis for

[gmx-users] Residue renaming during mdrun

All, I have a system of nitric acid modelled as NO3- and HO3+ plus SPC water. After setting the system up using genbox I then energy minimise. Althouth the input conf.gro file looks fine (NO3- labelled 'NO3', HO3+ labelled 'HO3' and water labelled 'SOL') the confout file has all of the H3O

[gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be

Dear, i want to study how ligands change the conformations using the gromacs software and i want to run 100ns, but i don't konw how to reasonably set the nstxout nstvout nstenergy nstlog and nstxtcout. Thank you very much! -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] mdrun and simulation time

Good morning all, This morning I checked the output of a 8ns (4 x 2ns) of simulation and I noticed a strange behaviour: The fist two simulations (each 2ns) ended up correctly and they both took 2h 06min to finish. The second two were still running when the cluster time was over (I asked for 2.30)

[gmx-users] Re: umbrella sampling

Hi, it seems that you've only coupled your protein to the thermostat, but not the solvent, hence the error message. Generally one would couple both domains of the protein to one thermostat and the solvent (inluding ions) to another thermostat. Side note: If you want to use the WHAM method for

Re: [gmx-users] Initial velocity

On 5/13/13 1:48 AM, Acoot Brett wrote: Dear All, Will you please explain how the initial velocity may affect the MD results? We use different initial velocities to improve sampling, i.e. to allow the trajectory to evolve in different ways. In the end, in the limit of infinite sampling,

Re: [gmx-users] Issue running gromacs in Cluster

On 5/13/13 4:44 AM, Sainitin Donakonda wrote: Thank you very much for inputs but i forgot to mention in previous query i got one error ..with other protein ligand simulation i used same MD file saving 200 steps.. *Cannot write trajectory frame; maybe you are out of quota?* * * Whats the

Re: [gmx-users] Center of Mass (COM) spacing between protein and ligand

On 5/13/13 5:33 AM, Arunima Shilpi wrote: Respected Sir many many thanks for your reply to my last mail. I was able able to debug the error Here I have new set of queries.. How much COM spacing should i consider for my protein-ligand interactiom How much total distance I should move along

Re: [gmx-users] air-water-interface

On 5/13/13 6:10 AM, Nawel Mele wrote: Hi all, I am performing a simulation of protein at air/water interface. For create an air-water interface I just expand the box in the z direction. So,aAfter minimization we can noticed that water molecules moved out of bulk water in the z direction.

Re: [gmx-users] Residue renaming during mdrun

On 5/13/13 6:30 AM, Laura Leay wrote: All, I have a system of nitric acid modelled as NO3- and HO3+ plus SPC water. After setting the system up using genbox I then energy minimise. Althouth the input conf.gro file looks fine (NO3- labelled 'NO3', HO3+ labelled 'HO3' and water labelled

Re: [gmx-users] mdrun and simulation time

On 5/13/13 6:41 AM, Francesco wrote: Good morning all, This morning I checked the output of a 8ns (4 x 2ns) of simulation and I noticed a strange behaviour: The fist two simulations (each 2ns) ended up correctly and they both took 2h 06min to finish. The second two were still running when the

[gmx-users] Fw: probability from COM of micelle

- Forwarded Message - From: Justin Lemkul jalem...@vt.edu To: mohammad agha mra...@yahoo.com Cc: Sent: Monday, May 13, 2013 4:11 PM Subject: Re: probability from COM of micelle It is much better to post this information to the list so that others can benefit from it. -Justin On

Re: [gmx-users] air-water-interface

So we just compute an interface vacuum-water like the picture in attach in increase the coordinate value of the z-axis of the box? BUt I don't understand how just like that we creat an empty place and water move to this place?? 2013/5/13 Justin Lemkul jalem...@vt.edu On 5/13/13 6:10 AM,

[gmx-users] Fwd: electrostatic potential map

Dear All, I am running a simulation of ligand binding in a protein. Ligand is mostly negatively charged, so as expected it should bind to the positive region of the protein. To check the possible binding zone, I try to calculate or rather visualize the electrostatic potential map of a

Re: [gmx-users] air-water-interface

On 5/13/13 8:01 AM, Nawel Mele wrote: So we just compute an interface vacuum-water like the picture in attach in increase the coordinate value of the z-axis of the box? The list does not accept attachments. If you want to post an image or file, provide a public link to access it. BUt I

Re: [gmx-users] mdrun and simulation time

thank you for the reply, I'm in contact with my admin and I hope that he will tell me something soon. One thing that I really don't understand is why only the last nanoseconds are affected. I run the same simulation (with the same paramenters) and I've never had problems in the first 4 ns , only

Re: [gmx-users] air-water-interface

Thanks a lot for your answer. So by increasing the z coordinate after solvated the system we induce creation of a empty space above the solvated box. After minimisation a few water molecules move above its new empty space because their link are not strong enough. 2013/5/13 Justin Lemkul

Re: [gmx-users] issue in replica exchange

Ok, the redmine is filled up and anybody who has time to help finding the issue is welcome :) I can't do much more! As an alternative a colleague suggested that I could potentially get around the problem by using a compilation combining Open-MP or thread-MPI for each replica running on one

Re: [gmx-users] Initial velocity

Please thanks so much for your support but I still do not get what all you are talking about is On 13 May 2013 11:44, Justin Lemkul jalem...@vt.edu wrote: On 5/13/13 1:48 AM, Acoot Brett wrote: Dear All, Will you please explain how the initial velocity may affect the MD results?

Re: [gmx-users] Initial velocity

On 5/13/13 9:45 AM, Brighter Agyemang wrote: Please thanks so much for your support but I still do not get what all you are talking about is These posts are not related to your question. Reading posts on other topics can be very informative and should be augmented by literature and

[gmx-users] QM/MM simulations

Dear GROMACS support! For my experiment I should use QM/MM methods. For this reason I should link mdrun program with ORCA. I'm working with 4.6 gromacs version and doing following: download ORCA on my computer; set the flags: BASENAME=topol

[gmx-users] RDF - water and protein

Dear Gmx Users, I run long simulation of my protein with 50 small molecules in water. I calculated the RDF (Protein - Water) using -surf mol and -rdf mol_com. Please, take a look at my plot: http://speedy.sh/tmJbD/rdf-P-W.png Could you please, explain me why the second peak is so high? Shall I

Re: [gmx-users] QM/MM simulations

On 5/13/13 9:51 AM, DavidPO wrote: Dear GROMACS support! For my experiment I should use QM/MM methods. For this reason I should link mdrun program with ORCA. I'm working with 4.6 gromacs version and doing following: download ORCA on my computer; set the flags:

[gmx-users] REMD analysis

Dear Sir, I repeated the simulation again for 25 replicas with the following temp. distribution . 280 289.1 298.5 308.2 318.2 328.6 339.3 350.3 361.7 373.5 385.6 398.1 411.1 424.4 438.3 452.5 467.2 482.4 498.1 514.3 531.0 548.3 566.1 584.5 603.5 623.2 The output of md.log file is :- Replica

Re: [Spam:*****] [gmx-users] REMD analysis

You need to increase the temperature gaps indeed if you want acceptance ratio ~0.2/0.3. But again this won't work with the water … It is not clear what happens in your index file but probably a problem from grace to plot so many points … you can try to increase the Max drawing path length in

[gmx-users] Re: RDF - water and protein

Hi, the manual mentions that with the option '-surf' no normalization is done. So it's normal the RDF will inrease with larger distances, since the further you'll go away from the protein, the bigger the spherical shell is (from which the RDF for distance r is calculated) and the more water

Re: [gmx-users] how many nstxout nstvout nstenergy nstlog nstxtcout should be

As usual there is no universal question, it depends on what do you want to see from your MD. The main factor to consider is the disk space that you can use if you decide to save every 10 ps it means that for 100ns you'll have 10.000 frame, depending on your system this can be a huge amount of

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

So I think I figured out what was causing the discrepancy of Charmm27 energies between gromacs and NAMD. It appears that it's related to the gromacs version: energies from 4.5.7 and NAMD match very well while 4.6.1 gives energies that are different from both 4.5.7 and NAMD. Here are the

Re: [gmx-users] Comparing Charmm 27 energies from GROMACS and NAMD

Here is the script: #!/bin/bash # note: you must have par_all27_prot_lipid.prm in the starting directory set -e PROGRAMS=/g1/home/resal/Programs GMX_BIN_457=$PROGRAMS/gromacs/4.5.7/thread/bin GMX_BIN_461=$PROGRAMS/gromacs/4.6.1/thread/bin NMD_BIN=$PROGRAMS/namd/NAMD_2.9_Linux-x86_64-multicore

[gmx-users] Distance Restraints

Hi, I'm new to Gromacs. How to convert NMR paramagnetic relaxation enhancement distance restraints into gromacs format in topol.top file for structural MD refinement. --Rama -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-Restraints-tp5008207.html Sent from the

Re: [gmx-users] setting up a simulation of an ionic liquid

On 5/13/13 11:50 AM, Laura Leay wrote: All, I've seen a few threads about simulations in ionic liquds but have not come across anything that tells me what settings I should use in my mdp file. The system is nitric acid which has fully dissociated into NO3- and HO3+. The simulation will run

[gmx-users] Fwd: Rycaert-Bellemans function

Hello to all. I am simulating long-chain alcohols. For the dihedrals, I used Rycaert-Bellemans function. In this case I should delete the pairs from topology? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

Re: [gmx-users] Fwd: Rycaert-Bellemans function

On 5/13/13 6:24 PM, Marcelo Vanean wrote: Hello to all. I am simulating long-chain alcohols. For the dihedrals, I used Rycaert-Bellemans function. In this case I should delete the pairs from topology? That depends on which force field you are using. See manual section 4.2.12. -Justin --

RE: [gmx-users] Fwd: Rycaert-Bellemans function

That really depends on where the function that you are using comes from and what forcefield you are using (because each forcefield can treat them differently). If it is the one for alkane chains mentioned in the manual to be used with the GROMOS FFs, then as it states in the manual you have to

[gmx-users] Charge groups

Hi. I'm with doubts concerning the charge groups. I am simulating ethylene glycol and the only way of charged groups are neutral is putting all atoms in only one charge group. This is advisable? Is that a problem? What is the greatest number of atoms in a charge group which is recommended? --

Re: [gmx-users] Charge groups

On 5/13/13 8:23 PM, Marcelo Vanean wrote: Hi. I'm with doubts concerning the charge groups. I am simulating ethylene glycol and the only way of charged groups are neutral is putting all atoms in only one charge group. This is advisable? Is that a problem? What is the greatest number of atoms

Re: [Spam:*****] [gmx-users] REMD analysis

Dear Sir, Here's the result for the REMD trial with large temperature gaps. Temp. distribution : 280.0 294.9 310.7 327.3 344.7 363.1 382.5 402.9 424.4 447.1 471.0 496.1 522.6 550.5 579.9 610.8 Out of md16.log : Replica exchange statistics Repl 249 attempts, 125 odd, 124 even Repl average

[gmx-users] Large number of solvent molecules

Dear all, I am trying to see the folding of a 89 aa peptide. So I am setting up the system from linear conformation. I gave the following commands to build the box and add the solvent molecules. editconf -f output.gro -c -d 1.0 -bt dodecahedron -o outbox.gro genbox -cp outbox.gro -cs spc216.gro

RE: [gmx-users] Large number of solvent molecules

From the box volume printed in the script output it appears you have a box that is approximately a 28nm cube. And that size box requires a significant number of water molecules to fill up, so that number you have in there (~770,000) seems about correct. If you want to have less water

Re: [gmx-users] Large number of solvent molecules

Thank you Dr. Dallas. Yes I think the issue is that the starting conformation is linear, as I want to study its folding properties. I tried the same with helical starting conformation, and got around 11 water molecules, which is still ok. I am trying to find a way to simulate a 89 aa peptide