Re: [gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?

On 2010-10-22 00.49, Chih-Ying Lin wrote: Hi When I issued the command g_dipole, the dialog poped out and asked me to select a group. 1. system 2. protein . 11. solvent 12. the rest of the salt-molecule except its counter ion 13. counter ions (CL-) If I select #12, Gromacs will not

Re: [gmx-users] problem with energy groups and mdrun -rerun option

On 22/10/2010 8:21 AM, jagannath mondal wrote: Hi, I have used gromacs 4.0.7 to do MD simulation of two solutes A & B in water ( solvent) . Initially, I had set "energy groups = system " and used mdrun to do the simulation. Now,I wanted to get the potential energy contribution from due to

[gmx-users] g_dipole ? =>salt-molecule => Does Gromacs consider counter ions?

Hi When I issued the command g_dipole, the dialog poped out and asked me to select a group. 1. system 2. protein . 11. solvent 12. the rest of the salt-molecule except its counter ion 13. counter ions (CL-) If I select #12, Gromacs will not consider counter ions to calculate the di

Re: [gmx-users] GPU slower than I7

On Thu, Oct 21, 2010 at 5:53 PM, Renato Freitas wrote: > Thanks Roland. I will do a newer test using the fourier spacing equal > to 0.11. I'd also suggest to look at g_tune_pme and run with different rcoulomb, fourier_spacing. As long as the ratio is the same you get the same accuracy. And you s

RE: [gmx-users] molecular surface area(MSA)?

What you want then is a Connolly surface? Which I gather is what GROMACS actually calculates, http://www.mail-archive.com/gmx-users@gromacs.org/msg12518.html Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381

[gmx-users] molecular surface area(MSA)?

Hi,  I was wondering whether gromacs can calculate a quantity called molecular surface area(MSA) which is different from solvent accessible surface area(SASA). By definition, SASA of a molecule is the area of surface traced by center of a spherical water probe rolling on a vander wall surface of

Re: [gmx-users] GPU slower than I7

Thanks Roland. I will do a newer test using the fourier spacing equal to 0.11. However, about the performance of GPU versus CPU (mpi) let me try to explain it better: The simulation using gromacs with GPU started and finished: Started mdrun on node 0 Wed Oct 20 09:52:09 2010 Finished mdrun on nod

Re: [gmx-users] problem with energy groups and mdrun -rerun option

jagannath mondal wrote: Justin, Thanks for your reply. Then I wonder whether there is any other way out in gromacs to get the net interaction potential energy due to each of the components in a simulations. I am asking this, many times people report the potential energy contribution due

Re: [gmx-users] problem with energy groups and mdrun -rerun option

Justin,Thanks  for your reply.  Then I wonder whether there is any other way out in gromacs to get the net interaction potential energy due to each of the components in a simulations.  I am asking this, many times people report the potential energy contribution due to solvent-solvent interaction

Re: [gmx-users] problem with energy groups and mdrun -rerun option

jagannath mondal wrote: Hi, I have used gromacs 4.0.7 to do MD simulation of two solutes A & B in water ( solvent) . Initially, I had set "energy groups = system " and used mdrun to do the simulation. Now,I wanted to get the potential energy contribution from due to interaction of A-

[gmx-users] problem with energy groups and mdrun -rerun option

Hi,  I have  used gromacs 4.0.7 to do  MD simulation of two solutes A & B in water ( solvent) . Initially, I had set "energy groups = system " and used mdrun to do the simulation. Now,I wanted to get the potential energy contribution from due to interaction of  A-A, B-B,A-B A-solvent, B-solvent,

Re: [gmx-users] GPU slower than I7

On Thu, Oct 21, 2010 at 3:18 PM, Renato Freitas wrote: > Hi gromacs users, > > I have installed the lastest version of gromacs (4.5.1) in an i7 980X > (6 cores or 12 with HT on; 3.3 GHz) with 12GB of RAM and compiled its > mpi version. Also I compiled the GPU-accelerated > version of gromacs. The

Re: [gmx-users] rlist and rcoulomb

Swarnendu Tripathi wrote: Dear gromacs users, In section 4.6.3 of gromacs 4 manual it says ``... the interactions between pairs that do not fall within rlist but do fall within max(rcoulomb,rvdw) are computed during neighbor search (NS), and the forces and energy are stored separately, and

[gmx-users] rlist and rcoulomb

Dear gromacs users, In section 4.6.3 of gromacs 4 manual it says ``... the interactions between pairs that do not fall within rlist but do fall within max(rcoulomb,rvdw) are computed during neighbor search (NS), and the forces and energy are stored separately, and added to short-range forces at ev

Re: [gmx-users] Re: eigenvectors in readable format

In selecting the eigen vector i just want to make sure about my consideration about the time frames. Should i need to consider the time frame t= 0.0 or i need to start at non zero positive numbers? Thank you. Rama On Fri, Oct 15, 2010 at 11:00 PM, Tsjerk Wassenaar wrote: > Hi Rama, > > You can co

[gmx-users] g_dipole ? =>salt-molecule => the relative position of counter ions to the rest of salt-molecule matters ???

HI As Timo M.D. Graen described "As long as the system is neutral, the reference point will not affect the calculation result of the dipole moment for the system." On the other hand, I also play around the small salt-molecule as Timo M.D. Graen suggested. "take two ions for a start, Na+ and Cl-,

[gmx-users] GPU slower than I7

Hi gromacs users, I have installed the lastest version of gromacs (4.5.1) in an i7 980X (6 cores or 12 with HT on; 3.3 GHz) with 12GB of RAM and compiled its mpi version. Also I compiled the GPU-accelerated version of gromacs. Then I did a  2 ns simulation using a small system (11042 atoms)  to co

Re: [gmx-users] RE: Gibbs free energy of binding

reading your idea: it seems to me I can't ignore entropy contribution because my simulation is at room tempreture. Really I couldn't understand what can I do! I am working at room tempreture and I want to estimate binding free energy(delta G),can I ignore entropy in this simulation and calculate b

[gmx-users] g_dipole ? => dipole moment => trans-structure is more hydrophobic than the cis-structure ?

Hi In one paper, the salt-molecule has two structures, trans and cis. The sentence in the paper is that trans-structure is more hydrophobic than the cis-structure without providing the value of the dipole moment. I wonder know if the value of dipole moment is the main indicator to decide if tran

[gmx-users] Problems with NVT simulation with CHARMM27

Dear All, I am trying to equilibrate in NVT ensemble of a peptide with glycolipid (GL) molecules in a cubic box filled with TIP3P water (from Mackerell et al.). The force field for GL were converted to GROMACS format from CHARMM27 force field with additional parameters non present in the forcefiel

[gmx-users] g_dipole ? => The salt molecule => The discrepancy of dipole moment between my calculation and GROMACS

HI dipole moment = 48.0 sum of q_i x_i x_i is the atomic position. The PBC is considered. I did not include the counter ion of the salt molecule in my calculation. The salt molecule is A-N(CH3)3-Br and it has two structures, cis and trans. Here "A" are a string of atoms, most of them are carbons

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

Hi, FWIW, I have recently asked about this in the hwloc mailing list: http://www.open-mpi.org/community/lists/hwloc-users/2010/10/0232.php In general, hwloc is a useful tool for these things. http://www.open-mpi.org/projects/hwloc/ Best, Ondrej On Thu, Oct 21, 2010 at 12:03, Carsten Kutzner

Re: [gmx-users] CHARMM36 lipid bilayers

Hi Sven, I have also seen similar things from the area per lipid of the bilayers I have run (POPC and DPPC). I would suggest you try running with the CHARMM TIP3P water (tips3p.itp) and see if you get values which are closer to the ones published in the paper you mention. This will be discussed i

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

>>> Thanks for the information; the OpenMPI recommendation is probably because >>> OpenMPI goes to great lengths trying to avoid process migration. The >>> numactl doesn't prevent migration as far as I can tell: it controls where >>> memory gets allocated if it's NUMA. >> My understanding is t

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

On 21 Oct 2010, at 16:50 , Carsten Kutzner wrote: > On Oct 21, 2010, at 4:44 PM, Sander Pronk wrote: > >> >> Thanks for the information; the OpenMPI recommendation is probably because >> OpenMPI goes to great lengths trying to avoid process migration. The numactl >> doesn't prevent migration

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

On Oct 21, 2010, at 4:44 PM, Sander Pronk wrote: > > Thanks for the information; the OpenMPI recommendation is probably because > OpenMPI goes to great lengths trying to avoid process migration. The numactl > doesn't prevent migration as far as I can tell: it controls where memory gets > alloc

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

Thanks for the information; the OpenMPI recommendation is probably because OpenMPI goes to great lengths trying to avoid process migration. The numactl doesn't prevent migration as far as I can tell: it controls where memory gets allocated if it's NUMA. For gromacs the setting should of cours

Re: [gmx-users] (no subject)

On 22/10/2010 1:17 AM, Nilesh Dhumal wrote: I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE char

Re: [gmx-users] (no subject)

Nilesh Dhumal wrote: I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on sol

Re: [gmx-users] (no subject)

I am doing solvation dynamics for my system. I have system with diatomic (PA---NE)solute surrounded by water molecules. I want to run simulation with two differcent cases. 1. PA charge=0 and NE charge=0 : No charge on solute 2. PA charge=+1 and NE charge=-1 : Charge on solute I want to calculate

Re: [gmx-users] (no subject)

On 21/10/2010 11:55 PM, Nilesh Dhumal wrote: Hello, I am working on a system which has a diatomic solute surrounded by water molecules. I want to calculate the energy for each step with and with out charge on solute simultaneously. Pl. help me solve this problem. I don't understand what you wan

Re: [gmx-users] CHARMM36 lipid bilayers

Hi Berk, the original charmm article used rvdw=1.2 rvdw_switch=0.8 coulombtype= PME Unfortunately, they did not specify rcoulomb explicitly. In the discussions they wrote ".. simulations of bilayers with C36 should be carried out with PME with rc=10 or 12 A and no long-range corrections for the

[gmx-users] (no subject)

Hello, I am working on a system which has a diatomic solute surrounded by water molecules. I want to calculate the energy for each step with and with out charge on solute simultaneously. Pl. help me solve this problem. Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.groma

RE: [gmx-users] CHARMM36 lipid bilayers

Hi, You have very strange and complex cut-off settings in Gromacs. What Charmm settings are you trying to mimic? Berk > Date: Thu, 21 Oct 2010 15:03:51 +0200 > From: jakobtorwei...@tuhh.de > To: gmx-users@gromacs.org > Subject: [gmx-users] CHARMM36 lipid bilayers > > Dear gmx-users, > > recen

[gmx-users] (no subject)

Hello, I am working on a system which has a diatomic solute surrounded by water molecules. I want to calculate the energy for each step with and with out charge on solute simultaneously. Pl. help me solve this problem. Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.grom

[gmx-users] gromacs+MOPAC QMMM error

I have compiled a mdrun version of gromacs 4.0.7 linked with the mopac7 libraries, as described in the tutorial: *** export CC=gcc export CXX=g++ export F77=gfortran export MPICC=/apps/openmpi/1.4.2/gcc/bin/mpicc export CPPFLAGS="-DUSE_MOPAC -I/apps/fftw/3.2.2/gcc/include -I/apps/gsl/1.9/gcc/in

[gmx-users] CHARMM36 lipid bilayers

Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files for Charmm36 lipids. I run some simulations to find the best run parameters and to check if the results of the original Charmm36 lipid article [Klauda et al., J. Phys Chem. B, 2010, 114, 7830) can be reproduce

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

vinothkumar mohanakrishnan wrote: Hi Justin Thank you for your suggestion. I am doing equilibration of DCE (108 molecules) alone in a box and there is no water molecule inside the box. cant i use -DFLEXIBLE for DCE?. by the way i will try your suggestion about xmgrace. In that case, -DF

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

Hi Sander, On Oct 21, 2010, at 12:27 PM, Sander Pronk wrote: > Hi Carsten, > > As Berk noted, we haven't had problems on 24-core machines, but quite frankly > I haven't looked at thread migration. I did not have any problems on 32-core machines as well, only on 48-core ones. > > Currently, th

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

vinothkumar mohanakrishnan wrote: Hi Justin Below is my nvt.mdp (nvt equilibration) file.i think probably you can have look at it and its not such big. define = -DFLEXIBLE You should never run MD with flexible water. All the water models included in Gromacs are

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

Hi Justin Below is my nvt.mdp (nvt equilibration) file.i think probably you can have look at it and its not such big. define = -DFLEXIBLE integrator = md nsteps = 5 dt= 0.002 nstxout

RE: [gmx-users] Re: published paper related to protein simulation, using gromacs

Hi, I think, started from some gromacs tutorial is a nice ideas and then during those process you certainly will meet some paper. lina From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Thomas Schlesier [schl...@uni-mainz.d

[gmx-users] Re: published paper related to protein simulation, using gromacs

Hi, use ISI Web of Knowledge or scholar.google, search for 'protein + gromacs' and you should get tons of results. Greetings Thomas Date: Thu, 21 Oct 2010 13:29:11 +0300 From: ahmet y?ld?r?m Subject: [gmx-users] published paper related to protein simulation using gromacs To: Discuss

Re: [gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

Karel Berka wrote: Karel Berka wrote: > Hi all, > > I have detected that preference in reading forcefield files in Gromacs > 4.5 has probably been changed from Gromacs 4.0.x and older. > In older gromacs, when there was forcefield with modification present

Re: [gmx-users] published paper related to protein simulation using gromacs

Ahmet, For starting you can read Leach's book (Molecular modeling: principles and applications). This book gives you theoretical background and opinion about application areas of molecular dynamics (MD) simulation. Gromacs is only a simulation tool to do MD simulation, after understanding MD you

Re: [gmx-users] Reg: Running Energy minimisation for dichloroethane (DCE)

vinothkumar mohanakrishnan wrote: Hi justin I found what went wrong and i corrected my mdp file.now the system equilibrated to the desired temperature 300 K (plus r minus 30 K) is this ok? This is impossible to assess without seeing your .mdp settings. A fluctuation of 10% is probably fi

Re: [gmx-users] Force-field files location and order of reading in Gromacs 4.5.2

> > > Karel Berka wrote: > > Hi all, > > > > I have detected that preference in reading forcefield files in Gromacs > > 4.5 has probably been changed from Gromacs 4.0.x and older. > > In older gromacs, when there was forcefield with modification present in > > my working directory, then it was read

[gmx-users] published paper related to protein simulation using gromacs

Dear Gromacs users, I am new user Gromacs. I want to study on protein simulation using gromacs. If possible, Can you send a few articles on the protein simulation using Gromacs?For example, I downloaded from Protein Data Base the PDB extension file of any protein. What is the purpose of protein si

Re: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

Hi Carsten, As Berk noted, we haven't had problems on 24-core machines, but quite frankly I haven't looked at thread migration. Currently, the wait states actively yield to the scheduler, which is an opportunity for the scheduler to re-assign threads to different cores. I could set harder thr

RE: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

Hi, We haven't observed any problems running with threads over 24 core AMD nodes (4x6 cores). Berk > From: ckut...@gwdg.de > Date: Thu, 21 Oct 2010 12:03:00 +0200 > To: gmx-users@gromacs.org > Subject: [gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs > > Hi, > > does anyone have experie

[gmx-users] Gromacs 4.5.1 on 48 core magny-cours AMDs

Hi, does anyone have experience with AMD's 12-core Magny-Cours processors? With 48 cores on a node it is essential that the processes are properly pinned to the cores for optimum performance. Numactl can do this, but at the moment I do not get good performance with 4.5.1 and threads, which still

[gmx-users] RE: Gibbs free energy of binding

Hi, Under constant pressure a potential energy change is in many cases a good approximation for the change of enthalpy (if only small variations of volume are present). However, for many biomolecular applications, and in particular ligand binding, the entropy contribution cannot be neglected un

Re: [gmx-users] RE: Gibbs free energy of binding

To put some numbers to what David said, here's an experimental paper on a well-studied drug-protein complex: http://pubs.acs.org/doi/pdf/10.1021/bi001013s the entropic contribution of HIV-1 protease inhibitor binding is about 3x bigger than the enthalpic contribution for all 4 drugs studied ther

Re: [gmx-users] RE: Gibbs free energy of binding

On 2010-10-21 10.39, Ehud Schreiber wrote: Actually, I believe that using the energy difference, Delta E, as an approximation to the free energy difference, Delta G, is a valid approach (which I'm considering myself). The entropic contribution to Delta G, namely -T Delta S, may be less prominent

[gmx-users] RE: Gibbs free energy of binding

Actually, I believe that using the energy difference, Delta E, as an approximation to the free energy difference, Delta G, is a valid approach (which I'm considering myself). The entropic contribution to Delta G, namely -T Delta S, may be less prominent than Delta E. In addition, Delta S can be app

Re: [gmx-users] g_dipole ? => salt molecule in water => what is the the displacement vector pointing from the negative charge to the positive charge?

reconsider your statement about the displacement vector. You should try to understand the concepts of vectors and reference points first. It is absolutely mandatory to do so before calculating dipole moments of charged systems. It might also be wise to use a small test system to practice on. Fo

Re: [gmx-users] Gibbs free energy of binding

Hi Mohsen, The mean energy difference is only one component of the free energy difference. Before you go any further I'd suggest reading a good book on molecular simulations, like 'Understanding Molecular Simulations' by Frenkel and Smit. There's a good reason free energy calculations cover o

Re: [gmx-users] Gibbs free energy of binding

Dear Justin If I do two MD simulations for a short time in the same conditions(of course separately for protein and drug) and calculate total energy of each one and sum them with each other as E1 as nonbonding free energy of system. then a MD simulation for Protein-drug system in the same condi