[gmx-users] remd

Sir, I did an 80 ns Remd simulation, after completion of the simulation extended it up to 480 ns using tpbconv. Now the extended trajectories also write on old trajectory files(traj.trr)? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users *

Re: [gmx-users] Regarding g_order

Thanks Justin for the quick reply. I am simulating a protein with bound lipids. I am in a dilemma to choose the direction of the normal to calculate order parameter. In your *Membrane-protein *simulation tutorial, you have chosen normal to the bilayer along the z-axis. But in my case, there is no b

Re: [gmx-users] Potential Energy Scan

Thank you Mark. So, if I got it properly, for my system (dihedral scanning), I need to generate configurations, manually, and then perform this 'single point energy calculations' for each of the configurations. If so, then better I would opt for a script to do my job. Regards, Tarak On Thu, Aug

[gmx-users] Trying to explain differences in behaviour between 2fs and 5fs timesteps

Hi all, I've been running an analysis of the same system (protein/ligand/water/ions) using multiple timesteps (1-5fs) to identify differences in behaviour between the settings. To do this I've compared the energy outputs of the 5 simulations, specifically the averages from g_energy and binning the

[gmx-users] COM of a molecule

Hi I want to determine center of mass position of a molecule given an index of any of the atoms of the molecule. One may be able to do this if given an atom index one can access indices and hence the position of all other atoms belonging to the same molecule. Is there a way to do this in a program

Re: [gmx-users] g_potential and trjconv: problems with bilayer simulation analysis

On 8/1/13 6:55 PM, wood irene wrote: Hi all I'm trying to calculate the electrostatic potential of POPC membrane systems from a trajectory. When I use g_potential, the calculation is well done but the results are plotted from 0 to 7 nm of Z coordinates, with the bilayer center near to 3.5nm. Is

[gmx-users] g_potential and trjconv: problems with bilayer simulation analysis

Hi all I'm trying to calculate the electrostatic potential of POPC membrane systems from a trajectory. When I use g_potential, the calculation is well done but the results are plotted from 0 to 7 nm of Z coordinates, with the bilayer center near to 3.5nm. Is possible, modifying the trajectory in or

Re: [gmx-users] Re: inconsistent energy drops

On 8/1/13 5:18 PM, Brad Van Oosten wrote: To be honest, i have not updated that box to the newest version. If it appears to be a serious bug i could do it and rerun these sims to see if it does persist. I think it is worth doing. If -rerun calculates sensible energies but the original sim

[gmx-users] Re: inconsistent energy drops

To be honest, i have not updated that box to the newest version. If it appears to be a serious bug i could do it and rerun these sims to see if it does persist. -- View this message in context: http://gromacs.5086.x6.nabble.com/inconsistent-energy-drops-tp5010260p5010299.html Sent from the GRO

Re: [gmx-users] Re: inconsistent energy drops

On 8/1/13 5:08 PM, Brad Van Oosten wrote: This was done on v 4.6.1 Does the same problem persist in 4.6.3? -Justin md50.mdp: title= MD simulation integrator = md ; MD integrator tinit= 0 dt = 0

[gmx-users] Re: inconsistent energy drops

This was done on v 4.6.1 md50.mdp: title= MD simulation integrator = md ; MD integrator tinit= 0 dt = 0.002; 2 fs timestep nsteps = 5000 ; Number of st

Re: [gmx-users] Re: inconsistent energy drops

On 8/1/13 4:58 PM, Brad Van Oosten wrote: I used the mdrun -rerun option to recalculate the energies of the system and it gave me nearly the same energy plot but without the random drops(see plot below). I am still unsure what is causing the jumps but i do not believe it is from my system. Si

Re: [gmx-users] 1. Re: Interaction energy between specific residue in a set of residues (Justin Lemkul)

On 8/1/13 4:55 PM, Collins Nganou wrote: Dear Justin, Thanks I am simulating a DNA with different residues. I am looking the way to extract only the energy of adjacent DT. I intend print out this energy group via the energygrps = DT I would like to have only DT in the index file. But it d

[gmx-users] Re: inconsistent energy drops

I used the mdrun -rerun option to recalculate the energies of the system and it gave me nearly the same energy plot but without the random drops(see plot below). I am still unsure what is causing the jumps but i do not believe it is from my system. Since the energy is used in the calculation for

[gmx-users] 1. Re: Interaction energy between specific residue in a set of residues (Justin Lemkul)

Dear Justin, Thanks I am simulating a DNA with different residues. I am looking the way to extract only the energy of adjacent DT. I intend print out this energy group via the energygrps = DT I would like to have only DT in the index file. But it doesn't work. This is the error encounter:

Re: [gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher

On 8/1/13 4:10 PM, akk5r wrote: Hi All, I am trying to run a membrane protein simulation on Gromacs 4.6 using the Charmm 36 force field parameters. I found the following parameters on the gromacs mailing list for Charmm 36: *; nblist cut-off rlist= 1.2 ; long-range cut-off

Re: [gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher

Hi, just try to disable OpenMP threads, unsetting OMP_NUM_THREADS environment variable Francesco 2013/8/1 akk5r > Hi All, > > I am trying to run a membrane protein simulation on Gromacs 4.6 using the > Charmm 36 force field parameters. > > I found the following parameters on the gromacs mailin

[gmx-users] Using Charmm 36 forcefield on Gromacs 4.6 or higher

Hi All, I am trying to run a membrane protein simulation on Gromacs 4.6 using the Charmm 36 force field parameters. I found the following parameters on the gromacs mailing list for Charmm 36: *; nblist cut-off rlist= 1.2 ; long-range cut-off for switched potentials rlistlo

Re: Re: Re: [gmx-users] GPU-based workstation

I may be late with the reply, but here are my 2 cents. If you need a single very fast machine (i.e. maximum single simulation performance), you should get - either a very fast desktop CPU: i7 3930 or for 2x more the 3970 - which, BTW, I think is not worth it ($600-1000) - or 1-2 fast Xeon E5-s - d

Re: [gmx-users] Regarding g_order

On 8/1/13 12:07 PM, Venkat Reddy wrote: Dear Gmx-users, In the GROMACS site, it has been mentioned that there is a bug (Instead of numbering carbons from 2-17, the numbering starts from 1-16) in g_order program up to, and including, v4.5.4. But when I am using v4.5.5, I am getting the same sort

Re: [gmx-users] Intel vs gcc compilers

Hi, The Intel compilers are only recommended for pre-Bulldozer AMD processors (K10: Magny-Cours, Intanbul, Barcelona, etc.). On these, PME non-bonded kernels (not the RF or plain cut-off!) are 10-30% slower with gcc than with icc. The icc-gcc difference is the smallest with gcc 4.7, typically arou

Re: [gmx-users] concatenating 2 xtc files

On 8/1/13 11:44 AM, Kavyashree M wrote: Sir, Thank you for the suggestion.. I will make use of it in future runs. but now the simulation is over. But if something went wrong, then "over" is rather irrelevant, isn't it? There was some overlap of few ns in 8core machine. so while checking t

Re: [gmx-users] Box dimension size errors in MARTINI soft core simulation

On 8/1/13 11:35 AM, Scott Pendley wrote: Justin, Much appreciation for the suggestions. I found that the large time constant (tau_p) on the pressure coupling was indeed a significant contributor. When I dropped that value down to 2.5, the box vectors scaled down in a more reasonable manner m

Re: [gmx-users] Re: CUDA with QUADRO GPUs

Dear Ramon, Thanks for the kind words! On Tue, Jun 18, 2013 at 10:22 AM, Ramon Crehuet Simon wrote: > Dear Szilard, > Thanks for your message. Your help is priceless and helps advance science > more than many publications. I extend that to many experts who kindly and > promptly answer question

[gmx-users] Regarding g_order

Dear Gmx-users, In the GROMACS site, it has been mentioned that there is a bug (Instead of numbering carbons from 2-17, the numbering starts from 1-16) in g_order program up to, and including, v4.5.4. But when I am using v4.5.5, I am getting the same sort of numbering. Is it normal or I should renu

Re: [gmx-users] concatenating 2 xtc files

Sir, Thank you for the suggestion.. I will make use of it in future runs. but now the simulation is over. There was some overlap of few ns in 8core machine. so while checking the rmsd plot there was a significant difference in rmsd between 8 core and 64 core overlapped region of simulation. 1 mo

Re: [gmx-users] Box dimension size errors in MARTINI soft core simulation

Justin, Much appreciation for the suggestions. I found that the large time constant (tau_p) on the pressure coupling was indeed a significant contributor. When I dropped that value down to 2.5, the box vectors scaled down in a more reasonable manner maintaining the cubic simulation box. With re

Re: [gmx-users] fatal error with charmm/amber forcefield

On Wed, Jul 31, 2013 at 11:20 PM, Sanku M wrote: > Dear Gromacs users, > I am using gromacs 4.5.4 . > Is there any known issue/problem in running hamiltonian replica exchange > calculations or FEP with charm27.ff or amber forcefield in gromacs4.5.4 ? Almost certainly. Do check out the relea

Re: [gmx-users] concatenating 2 xtc files

On 8/1/13 3:42 AM, Kavyashree M wrote: Dear Sir, First trajectory - traj1.xtc (0 to 5... ns) Second trajectory - traj2.xtc (5... to 25ns) But there is no gap in between. for concatenating - $ trjcat -f traj1.xtc traj2.xtc -o trajf.xtc For nujump - $ trjconv -f trajf.xtc -s md.tpr -pbc nojum

Re: [gmx-users] Potential Energy Scan

http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy On Thu, Aug 1, 2013 at 7:03 AM, tarak karmakar wrote: > Dear All, > > Can anyone guide me how to perform the 'potential energy scan' for a > dihedral of a small molecule in gromacs? > > Regrads, > Tarak > -- > gmx-users mailing list

Re: [gmx-users] Re: Conserved energy ("Conserved En.") in NVT simulation

On Wed, Jul 31, 2013 at 9:42 PM, Janne Hirvi wrote: > Thanks for your comments Mark, > > If I understood correctly, you are saying, that maybe linear drift in > "Conserved En." could indicate conservation of > that quantity, which we actually should be interested. > > However, I made meanwhile so

[gmx-users] Re: Energies in MM scanning using gmx

Thank you, all! I know the reason now! All the best, qh -- View this message in context: http://gromacs.5086.x6.nabble.com/Energies-in-MM-scanning-using-gmx-tp5010274p5010278.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@grom

[gmx-users] QM/MM with gromacs 4.5.5-gaussian03

Hi all.I'm trying to run a test QM/MM calculation of Pd2+ in water using gromacs-4.5.5+gaussian03 and it results in folowing error messages: 225409.err (MDP file is here: fep.mdp

[gmx-users] Re: fftw

atila petrosian wrote > Dear gromacs users > > > Why should I install fftw before gromacs installation? > > I want to know exact role of fftw in gromacs calculations. > > Please guide me about that. > > Best wishes > -- > gmx-users mailing list > gmx-users@ > http://lists.gromacs.org/ma

Re: [gmx-users] concatenating 2 xtc files

Dear Sir, First trajectory - traj1.xtc (0 to 5... ns) Second trajectory - traj2.xtc (5... to 25ns) But there is no gap in between. for concatenating - $ trjcat -f traj1.xtc traj2.xtc -o trajf.xtc For nujump - $ trjconv -f trajf.xtc -s md.tpr -pbc nojump -o trajf.xtc I also have a case where I

[gmx-users] Energies in MM scanning using gmx

Dear all, But I have questions about the energies calculated by GMX for bonds and angles scanning. For example, a series of conformations of one system should be generated for a bond scanning, the only difference in geometry of these conformations is the bond length A---B. However, when I set the