[gmx-users] About gpu

I have tested gromacs-4.6.1 with k20. But when I run the mdrun, I met some problems. 1.Configure options are -DGMX_MPI=ON ,-DGMX_DOUBLE=ON -DGMX_GPU=OFF . But if I run parallely with mpirun, it would get wrong. Note: file tpx version 58, software tpx version 83 Fatal error in PMPI_Bcast:

[gmx-users] thermal conductivity,specific heat,enthalpy

Dear users, I calculated diffusion constant of a substance using g_msd tool. I also want to calculate thermal conductivity its. By the way,I did npt simulation. Diffusion constant=alpha Thermal conductivity=k specific heat=Cp density=d alpha=k/(d.Cp) and k=alpha.d.Cp I need d and Cp to

[gmx-users] Viscosity calculation using cos_acceleration

Dear Gromacs users, This question seems to come up periodically in the mailing list, but none of the previous answers seem helpful in my case. I'm trying to reproduce the viscosity calculation of SPC water by Berk Hess (JCP 116, 2002) using cos_acceleration in Gromacs. The answer I get is 2

[gmx-users] About parallelization

How to run combinedMPI/OPENMP parallelization with 2 or 4 Openmp threads per MPI process? -DGMX_MPI and -DGMX_THREAD_MPI can be use at the same time? How to run? Thanks for you help! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

[gmx-users] shall we add ions in FEP?

Hello: I found that in the free energy calculation tutorial, the ligand was placed in pure solvent which doesn't have any ions. I am just wondering, will it be better to add 0.15 M NaCl in the system especially when we would like to calculate protein/ligand binding energy through FEP?

[gmx-users] Charges for calculation of Coulomb interaction

Dear GMX users, Just a simple question, are the Coulomb interactions calculated using charges from ffnonbonded.itp or aminoacid.rtp? Normally, they are the same. However, if I modify some charges for some atoms (for example CB) of some residues in the aminoacid.rtp, but do not modify in

Re: [gmx-users] Maximum protein size for REMD?

I understand the point now. Bigger the system, closer will be the spacing. One thing though: The average energy (mu) returned by the web server for each temperature is 7-8 times more than the actual energy returned after REMD was over. Is there something we are missing here? Thanks. On Tue, Apr

[gmx-users] mdrun -rdd and -dds flag

Dear gmx-users, I am having a problem with a periodic molecule and the domain decomposition, I wish to use a high number of processors (circa 180, but can obviously be reduced) and therefore need to use the -rdd or -dds flags (I believe), how do these value effect the simulation? The box size

Re: [gmx-users] Re: Re: help: load imbalance (Justin Lemkul)

On Thu, Apr 11, 2013 at 1:12 AM, 申昊 shen...@mail.bnu.edu.cn wrote: Hello, I wanna ask some questions about load imbalance. 1 Here are the messages resulted from grompp -f md.mdp -p topol.top -c npt.gro -o md.tpr NOTE 1 [file md.mdp]: The optimal PME mesh load for

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

On Thu, Apr 11, 2013 at 1:56 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, I am trying MD simulation of tip5p water model. I am getting Fatal Error:Atomtype LP1 not found. There isnt LP in atomtypes.atp file. Which one corresponds to LP1 and LP2 atoms in atomtypes.atp file? (I

Re: [gmx-users] Charges for calculation of Coulomb interaction

On Thu, Apr 11, 2013 at 5:09 AM, fantasticqhl fantastic...@gmail.comwrote: Dear GMX users, Just a simple question, are the Coulomb interactions calculated using charges from ffnonbonded.itp or aminoacid.rtp? Normally, they are the same. However, if I modify some charges for some atoms

Re: [gmx-users] mdrun -rdd and -dds flag

On Thu, Apr 11, 2013 at 6:17 AM, manara r. (rm16g09) rm16...@soton.ac.ukwrote: Dear gmx-users, I am having a problem with a periodic molecule and the domain decomposition, I wish to use a high number of processors (circa 180, but can obviously be reduced) and therefore need to use the -rdd

Re: [gmx-users] mdrun -rdd and -dds flag

On 11/04/2013 11:17, manara r. (rm16g09) rm16...@soton.ac.uk wrote: Dear gmx-users, I am having a problem with a periodic molecule and the domain decomposition, I wish to use a high number of processors (circa 180, but can obviously be reduced) and therefore need to use the -rdd or -dds flags

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

Dear Justin, I copied to gmx.ff it. You know the tip5p shows the general shape of the 5-site water models but the spc shows the general shape of the 3-site water models. Therefore I need tip5p.itp. How can you get it? 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 1:56 AM,

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear Justin, I copied to gmx.ff it. You know the tip5p shows the general shape of the 5-site water models but the spc shows the general shape of the 3-site water models. Therefore I need tip5p.itp. Is there going to

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from gromacs 4.0.7. are they wrong? 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 6:52 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear Justin, I copied to gmx.ff it. You know the tip5p shows the

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from gromacs 4.0.7. are they wrong? Well, they trigger a fatal error... Yes, they are wrong and newer versions of Gromacs are correct. -Justin

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

There isnt tip5p.itp and tip5p.gro at newer versions of Gromacs. I couldnt find them 2013/4/11 Justin Lemkul jalem...@vt.edu On Thu, Apr 11, 2013 at 7:12 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: I am simulating tip5p water. I found tip5p.gro and tip5p.itp files from gromacs 4.0.7.

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

On Thu, Apr 11, 2013 at 7:28 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: There isnt tip5p.itp and tip5p.gro at newer versions of Gromacs. I couldnt find them They're there. The tip5p.gro file is in $GMXLIB and tip5p.itp is in several force field subdirectories. $ ls -l *.ff/tip5p.itp

Re: [gmx-users] About gpu

On Thu, Apr 11, 2013 at 8:14 AM, 陈照云 chenzhaoyu...@gmail.com wrote: I have tested gromacs-4.6.1 with k20. But when I run the mdrun, I met some problems. 1.Configure options are -DGMX_MPI=ON ,-DGMX_DOUBLE=ON -DGMX_GPU=OFF . But if I run parallely with mpirun, it would get wrong. Note: file

Re: [gmx-users] Maximum protein size for REMD?

Maybe. Either the model in the server is inapplicable for your system, or you've input data for the model incorrectly. Mark On Thu, Apr 11, 2013 at 11:34 AM, Nikunj Maheshwari nixcrazyfor...@gmail.com wrote: I understand the point now. Bigger the system, closer will be the spacing. One

Re: [gmx-users] Re: Re: help: load imbalance

On Thu, Apr 11, 2013 at 7:07 AM, 申昊 shen...@mail.bnu.edu.cn wrote: Hello, I wanna ask some questions about load imbalance. 1 Here are the messages resulted from grompp -f md.mdp -p topol.top -c npt.gro -o md.tpr NOTE 1 [file md.mdp]: The optimal PME mesh load for

Re: [gmx-users] About parallelization

On Thu, Apr 11, 2013 at 11:05 AM, 陈照云 chenzhaoyu...@gmail.com wrote: How to run combinedMPI/OPENMP parallelization with 2 or 4 Openmp threads per MPI process? GMX_OPENMP is on by default, and works automatically (where it can). See

Re: [gmx-users] Simulation of the HEM-containing proteins

During the past few days I've tried to make parametrization of any heme-containing cythochromes and always failed with the huge errors about missing parameters. Could someone provide me with such params (i suppose it should be added to thebonded/non-bonded.itps of the force field besides the rtps)

[gmx-users] vdw-modifier in GROMACS 4.6.1.

Dear all I have started simulations with the GROMACS 4.6.1, but I am bit confused with the application of the vdw-modifier. As far as I understand, in the case of : vdw-type= cut-off vdw-modifier-Potential-Shift the result will be a LJ potential shifted by a constant in order to be zero at the

[gmx-users] cygwin_mpi_gmx installation

Dear gmx, I have installed mpich for MPI use in cygwin (Win 7 -64 bit) and encountered the following error : I dont understand what I am missing here? $ cmake .. -DGMX_MPI=ON -DGMX_BUILD_OWN_FFTW=ON -- The C compiler identification is GNU 4.8.0 -- Check for working C compiler:

Re: [gmx-users] vdw-modifier in GROMACS 4.6.1.

It probably shouldn't do anything. However, at least the documentation should be better here. Does it work? Does it differ from vdw-type= Switch vdw-modifier=None? Mark On Thu, Apr 11, 2013 at 2:13 PM, Chrisostomos Batistakis tomyvanba...@gmail.com wrote: Dear all I have started

[gmx-users] fake atoms creation and causes a 1-4 interaction between atoms warning

hi i am using gromacs 4.5 and i am trying to run an energy minimization and then temperature equilibration for a system of two charged plates plates solvented in water. the plates are made of fake atoms which has carbon atoms parameters, and a bond length of 0.2 nm. the plates are made from o

[gmx-users] K20 test

Hi! When I run gromacs-4.6.1 with k20. I meet a question. I have 6 nodes.And each node has one K20.And I use one process on one node with one gpu. But the test result shows that the runtime of one node is less than that of six nodes.Is the scalability of GPU not good? Thanks! -- gmx-users

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

I am simulating tip5p water. I got tip5p.gro from $GMXLIB 1.) editconf -f tip5p.gro -o protein.pdb 2.) pdb2gmx -f protein.pdb -o protein.gro -p protein.top 14 (OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)) Select the Water Model: 1: TIP4P TIP 4-point, recommended 2: TIP3P TIP

Re: [gmx-users] tip5p water model:Atomtype LP1 not found

On Thu, Apr 11, 2013 at 9:27 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: I am simulating tip5p water. I got tip5p.gro from $GMXLIB 1.) editconf -f tip5p.gro -o protein.pdb 2.) pdb2gmx -f protein.pdb -o protein.gro -p protein.top 14 (OPLS-AA/L all-atom force field (2001 aminoacid

Re: [gmx-users] Fwd: rmsd

Thankyou On Wed, Apr 10, 2013 at 11:30 PM, Justin Lemkul jalem...@vt.edu wrote: On Wed, Apr 10, 2013 at 10:43 AM, Preeti Choudhary preetichoudhary18111...@gmail.com wrote: -- Forwarded message -- From: Preeti Choudhary preetichoudhary18111...@gmail.com Date: Wed, Apr

Re: [gmx-users] K20 test

Hi, No, it just means that *your simulation* does not scale. The question is very vague, hence impossible to answer without more details However, assuming that you are not running a, say, 5000 atom system over 6 nodes, the most probable reason is that you have 6 Sandy Bridge nodes with 12-16

Re: [gmx-users] vdw-modifier in GROMACS 4.6.1.

Well, I haven't try it but I will. But indeed, it shouldn't give any difference. I agree the documentation needs to be improved there. Tommy 2013/4/11 Mark Abraham mark.j.abra...@gmail.com It probably shouldn't do anything. However, at least the documentation should be better here. Does it

Re: [gmx-users] Dihedral angle PCA

On 2013-04-10 08:33, anu chandra wrote: Dear Gromacs users, I would like to do side-chain dihedral angle PCA for my protein. The protein contains 293 residues. I came across an explanation about dihedral PCA in gromcas website ( http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA). Is it

[gmx-users] gmx4.6.1 performance problem CPU acceleration: NONE

Hello: I have installed GMX4.6.1 and GMX4.5.5 on the same cluster. There are 2 Xoen E5 2630CPU in one node on this cluster. I tested the performance of those two versions of GMX, found GMX4.6.1 only had 0.62 performance of GMX4.5.5. When I checked the .log file of GMX4.6.1, I found ...

[gmx-users] Normal Mode Analysis -- Expected Output

Hello, I am running a normal mode analysis on a ~1500AA protein with the following mdp parameters: Log file opened on Tue Apr 9 09:55:00 2013 Host: uv1 pid: 128985 nodeid: 0 nnodes: 64 Gromacs version:VERSION 4.6.1 Precision: double Memory model: 64 bit MPI library:

[gmx-users] Re:

Thank you for your response. I am running double precision gromacs and I have minimized my structure down to ~1 Fmax, so neither of those concerns should be a problem. On Thu, Apr 11, 2013 at 12:15 PM, abhijit Kayal abhijitchemi...@gmail.comwrote: in normal mode analysis you will get 3n

Re: [gmx-users] Normal Mode Analysis -- Expected Output

On 2013-04-11 17:57, Bryan Roessler wrote: Hello, I am running a normal mode analysis on a ~1500AA protein with the following mdp parameters: Log file opened on Tue Apr 9 09:55:00 2013 Host: uv1 pid: 128985 nodeid: 0 nnodes: 64 Gromacs version:VERSION 4.6.1 Precision: double

[gmx-users] Memory requirement to store trajectories

Hi I would like to determine an estimate of hard disk space required to perform a typical MD simulation using gromacs. To do so, I am thinking of first finding how many bytes are required to store single atom's position, velocity and force in .trr file for a single frame, and then determine total

Re: [gmx-users] Memory requirement to store trajectories

On 2013-04-11 20:30, Sikandar Mashayak wrote: Hi I would like to determine an estimate of hard disk space required to perform a typical MD simulation using gromacs. To do so, I am thinking of first finding how many bytes are required to store single atom's position, velocity and force in .trr

[gmx-users] Re: thermal conductivity,specific heat,enthalpy

could anybody help me please? 2013/4/11 Ahmet yıldırım ahmedo...@gmail.com Dear users, I calculated diffusion constant of a substance using g_msd tool. I also want to calculate thermal conductivity its. By the way,I did npt simulation. Diffusion constant=alpha Thermal conductivity=k

Re: [gmx-users] gmx4.6.1 performance problem CPU acceleration: NONE

On Thu, Apr 11, 2013 at 5:41 PM, Yorquant Wang wangy...@gmail.com wrote: Hello: I have installed GMX4.6.1 and GMX4.5.5 on the same cluster. There are 2 Xoen E5 2630CPU in one node on this cluster. I tested the performance of those two versions of GMX, found GMX4.6.1 only had 0.62

Re: [gmx-users] Memory requirement to store trajectories

Do a short simulation that will be representative. Measure. Use multiplication. Mark On Thu, Apr 11, 2013 at 8:30 PM, Sikandar Mashayak symasha...@gmail.comwrote: Hi I would like to determine an estimate of hard disk space required to perform a typical MD simulation using gromacs. To do

Re: [gmx-users] fake atoms creation and causes a 1-4 interaction between atoms warning

Like I said yesterday when you posted this question from a different email account... Your system is blowing up because it's unstable. Where did you get this protocol? I suggest starting by reproducing something similar that has been published :-) On Thu, Apr 11, 2013 at 3:11 PM, aviv naftaly

[gmx-users] updating amberff.03 files

Hello Gromacs Users, I am trying to update the contents of the top folder. I have parameters for a HEME residue that worked in gromacs 4.0.7, and we're now trying to update to gromacs 4.6.1 (long overdue), and need to migrate the parameters over to the new version. I have done the

Re: [gmx-users] Simulation of the HEM-containing proteins

Look in the literature... On Thu, Apr 11, 2013 at 2:12 PM, James Starlight jmsstarli...@gmail.comwrote: During the past few days I've tried to make parametrization of any heme-containing cythochromes and always failed with the huge errors about missing parameters. Could someone provide me

Re: [gmx-users] updating amberff.03 files

Type 9 was added at some point to GROMACS to make coping with AMBER and CHARMM easier. So you should just change your #defines from 3 to 9. See table in chapter 5. Or you could just leave your solution in the same form as you did for the 4.0.x GROMACS. Mark On Thu, Apr 11, 2013 at 10:36 PM,

Re: [gmx-users] updating amberff.03 files

Hi Mark, We'd like to use the Ryckaert-Bellemans dihedral types. Does 3 not work in the new version? Also, I took out the #define lines and replaced them with the actual atomtypes, because that didn't seem to work when I initially tried to add just the #define lines to the ffbonded.itp file.

Re: [gmx-users] updating amberff.03 files

On Thu, Apr 11, 2013 at 11:14 PM, Laura Kingsley lking...@purdue.eduwrote: Hi Mark, We'd like to use the Ryckaert-Bellemans dihedral types. Does 3 not work in the new version? Sorry, I was thinking of 4 and 9, which are basically interchangeable. The default for AMBER did change to 9 at

Re: [gmx-users] updating amberff.03 files

So if I'm understanding you correctly in the .rtp file under [ HEME ] [ dihedrals ] I should change: HP42 CBD CGD O1D HP42 CBD CGD O2D ... to HP42 CBD CGD O1D30.65270 1.95811 0.0 -2.61082 0.0 0.0 HP42 CBD CGD O2D30.65270

[gmx-users] g_enemat problem suggestion

Hi, I would to calculate the interaction energies between two polymer molecules (unit1 and unit2) and the Water_CL_NA So the combinations are: unit1-unit2, unit1-Water_CL_NA, unit2-Water_CL_NA. After reading the documentation it seemed the tool g_enemat might be able to do just that in one go.

[gmx-users] g_enemat problem suggestion

g_energy states all the groups missing by g_enemat are present in the energy file: 45 Coul-SR:unit1-unit1 46 LJ-SR:unit1-unit1 47 Coul-14:unit1-unit1 48 LJ-14:unit1-unit1 49 Coul-SR:unit1-unit2 50 LJ-SR:unit1-unit2 51 Coul-14:unit1-unit2

Re: [gmx-users] Dihedral angle PCA

Hi David, Thanks for the reply. I have not tried yet. Since I didn’t find query about the dihedral PCA in the mail list, I thought of confirm about the steps mentioned in the web site. Regarding the use of dihedral PCA, the protein with which I am working behave differently from others. From

Re: [gmx-users] gmx4.6.1 performance problem CPU acceleration: NONE

1. Hi Mark: As your suggestion, I reinstalled GMX4.6.1, when I run CMAKE using *$**cmake ../ \* *-DCMAKE_INSTALL_PREFIX=/public/software/gromacs-4.6_avx \* *-DGMX_MPI=ON \* *-DCMAKE_C_COMPILER=/public/software/mpi/openmpi-16-intel/bin/mpicc \* *