Re: [gmx-users] ngmx not installed in gmx4.6.1

Thanks David. It worked. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Wed, Jun 5, 2013 at 1:02 AM, Dr. Vitaly Chaban wrote: > I do not know about the newest versions, but in older ones ngmx was missed > when you did not have the lesstif library installed. > > > Dr. Vitaly Chaban > >

[gmx-users] restraints on water oxygen atoms

Dear gmx users, I have a POPC/peptide/water/ions system. I ran NVT and then NPT on my system. I'd prefer to run the equilibrium steps with position restraints on water oxygen atoms, because the water molecules penetrate the lipid bilayer when running the equilibrium and I don't want it to happe

RE: [gmx-users] Difference between the electrostatic treatments PME/Cut-offs and Reaction Field

"Problem" solved. Just as well I held off reporting the "issue" in full until I had explored everything, I would ended have look a bit stupid ;-) But asking the initial question helped direct my thinking to the reason. The issue was the difference in van der Waals cut off between the PME/Cut-o

[gmx-users] About coulmb & Vanderrwalls cutoff

Dear Justin thank you for your previous reply                     How can i check using th value 1.4 is harmless to My system Through g_energy ouput (potential.xvg) can i check (graphically) Thnaks In Advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/list

Re: [gmx-users] About coulmb & Vanderrwalls cutoff

On 6/4/13 9:48 PM, vidhya sankar wrote: Dear Justin Thank you for your Previous reply. As yo mailed me The Defaut Value for vandewalls and Electrostatics in GROMOS96 53A6 is PME option s_type = grid

[gmx-users] About coulmb & Vanderrwalls cutoff

Dear Justin  Thank you for your Previous reply.                                                                              As yo mailed me  The Defaut      Value for vandewalls and Electrostatics  in GROMOS96 53A6  is  PME option s_type    = grid  nstlist    = 5  rlist      = 0.9  rcoulomb 

Re: [gmx-users] pdb2gmx

On 6/4/13 12:05 PM, Valentina Erastova wrote: Hello all, I am converting a .pdb into .gro and .top and assigning ClayFF forcefield, that is not included in the gromacs. It's a strange FF as doesn't have ones between all of the atoms, just O-H but it has an angle between a metal and OH, ther

[gmx-users] Re: pdb2gmx

Hi Valentina The first lines of your rtp files should be something like this where you specify the type (function) of the interaction [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 5 921 3 1 0

Aw: Re: [gmx-users] GPU problem

  Thanks, thats exact what I was looking for.   Stephan Gesendet: Dienstag, 04. Juni 2013 um 22:28 Uhr Von: "Justin Lemkul" An: "Discussion list for GROMACS users" Betreff: Re: [gmx-users] GPU problem On 6/4/13 3:52 PM, lloyd riggs wrote: > Dear All or anyone, > A stupid question. Is ther

Re: [gmx-users] Re: oxidized lipid - Peroxidated lipid

On 6/4/13 3:10 PM, dariush wrote: Dear All, I need to use oxidized lipids in my system. Any suggestion for force field that I can use would be appreciated. Googling turns up useful stuff like http://www.sciencedirect.com/science/article/pii/S0006349507716752. -Justin -- ==

Re: [gmx-users] GPU problem

On 6/4/13 3:52 PM, lloyd riggs wrote: Dear All or anyone, A stupid question. Is there an script anyone knows of to convert a 53a6ff from .top redirects to the gromacs/top directory to something like a ligand .itp? This is usefull at the moment. Example: [bond] 6 7 2gb_5 to [b

Re: [gmx-users] High Initial generated Temp

On 6/4/13 12:51 PM, tarak karmakar wrote: Yeah! It is indeed a silly point to generate a velocity distribution at 0 K. ( Maxwell-Boltzmann will be in trouble) After the warm up, now let say my protein is in 300 K, can't I generate a velocity distribution at 300 k (using the keyword gen_vel = ye

Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q

On Tue, Jun 4, 2013 at 5:48 PM, Mark Abraham wrote: > > > > On Tue, Jun 4, 2013 at 4:50 PM, Jianguo Li wrote: > >> >> >> Thank you, Mark and Xavier. >> >> The thing is that the cluster manager set the >> minimum number of cores of each jobs in Bluegene/Q is 128, so I can not >> use 64 cores. But

RE:[gmx-users] GPU problem

  Dear All or anyone,   A stupid question.  Is there an script anyone knows of to convert a 53a6ff from .top redirects to the gromacs/top directory to something like a ligand .itp?  This is usefull at the moment.  Example:   [bond]     6 7 2    gb_5   to   [bonds] ; ai  aj  fu   

Re: [gmx-users] ngmx not installed in gmx4.6.1

I do not know about the newest versions, but in older ones ngmx was missed when you did not have the lesstif library installed. Dr. Vitaly Chaban On Tue, Jun 4, 2013 at 5:55 PM, Chandan Choudhury wrote: > Dear gmx users, > > I had installed gromacs 4.6.1 using cmake. All the binaries are

[gmx-users] Re: oxidized lipid - Peroxidated lipid

Dear All, I need to use oxidized lipids in my system. Any suggestion for force field that I can use would be appreciated. Thanks, Dariush -- View this message in context: http://gromacs.5086.x6.nabble.com/oxidized-lipid-Peroxidated-lipid-tp5008661p5008810.html Sent from the GROMACS Users Foru

Re: [gmx-users] problems with GROMACS 4.6.2

Just a few minor details: - You can set the affinities yourself through the job scheduler which should give nearly identical results compared to the mdrun internal affinity if you simply assign cores to mdrun threads in a sequential order (or with an #physical cores stride if you want to use Hyper

Re: [gmx-users] GPU problem

"-nt" is mostly a backward compatibility option and sets the total number of threads (per rank). Instead, you should set both "-ntmpi" (or -np with MPI) and "-ntomp". However, note that unless a single mdrun uses *all* cores/hardware threads on a node, it won't pin the threads to cores. Failing to

[gmx-users] problems with GROMACS 4.6.2

Hi GROMACS users, It's come to our attention that some changes we made in 4.6.2 to the way we detect low-level hardware attributes sometimes affects mdrun performance. Specifically: * using real MPI will likely lead to lower performance than 4.6.1, if GROMACS managing the setting of thread affinit

Re: [gmx-users] High Initial generated Temp

Yeah! It is indeed a silly point to generate a velocity distribution at 0 K. ( Maxwell-Boltzmann will be in trouble) After the warm up, now let say my protein is in 300 K, can't I generate a velocity distribution at 300 k (using the keyword gen_vel = yes, gen_temp = 300 K gen_seed = 173529 ) during

Re: [gmx-users] Can we connect two boxes together for the simulation?

Nohow. Numbers in GRO files serve exclusively decorative function. Dr. Vitaly Chaban On Tue, Jun 4, 2013 at 4:12 PM, Bao Kai wrote: > Hi, > > > I guess the renumbering of the atoms and molecules will be a problem, > especially when the two boxes contain the same type of the molecules. > >

Re: [gmx-users] GPU problem

On 06/04/2013 11:22 AM, Chandan Choudhury wrote: Hi Albert, I think using -nt flag (-nt=16) with mdrun would solve your problem. Chandan thank you so much. it works well now. ALBERT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Ple

Re: [gmx-users] High Initial generated Temp

On 6/4/13 12:17 PM, tarak karmakar wrote: Thanks Justin. Sorry for not uploading the full .mdp. Here it is, ; 7.3.3 Run Control integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps

Re: [gmx-users] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration

mdrun is not blind, just the current design does report the hardware of all compute nodes used. Whatever CPU/GPU hardware mdrun reports in the log/std output is *only* what rank 0, i.e. the first MPI process, detects. If you have a heterogeneous hardware configuration, in most cases you should be a

Re: [gmx-users] High Initial generated Temp

I'm extremely sorry for copying the other '.mdp' file here. This is the modified one I just created after seeing your reply. In the previous case I didn't use 'continuation'. On Tue, Jun 4, 2013 at 9:47 PM, tarak karmakar wrote: > Thanks Justin. > Sorry for not uploading the full .mdp. Here it

Re: [gmx-users] High Initial generated Temp

Thanks Justin. Sorry for not uploading the full .mdp. Here it is, ; 7.3.3 Run Control integrator = md tinit = 0 dt = 0.001 nsteps = 500 nstcomm = 1 comm_grps = system comm_mode = li

Re: [gmx-users] ngmx not installed in gmx4.6.1

This has been default behaviour for years. See pre-conditions here http://www.gromacs.org/Documentation/Installation_Instructions#.c2.a7_3.5._Optional_build_components. David's email has one way to solve the problem. Mark On Tue, Jun 4, 2013 at 5:55 PM, Chandan Choudhury wrote: > Dear gmx use

[gmx-users] pdb2gmx

Hello all, I am converting a .pdb into .gro and .top and assigning ClayFF forcefield, that is not included in the gromacs. It's a strange FF as doesn't have ones between all of the atoms, just O-H but it has an angle between a metal and OH, therefore I wore out molecule.rtp (see below) that i

Re: [gmx-users] ngmx not installed in gmx4.6.1

On 2013-06-04 17:55, Chandan Choudhury wrote: Dear gmx users, I had installed gromacs 4.6.1 using cmake. All the binaries are installed, but surprisingly I do not find ngmx executable. Can anyone guide me how do I install ngmx using cmake. cmake -DGMX_X11=ON Chandan -- Chandan kumar Choudhur

Re: [gmx-users] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration

Yes, documentation and output is not optimal. Resources are limited, sorry. Some of these issues are discussed in http://bugzilla.gromacs.org/issues/1135. The good news is that it sounds like you are having a non-problem. The output tacitly assumes heterogeneity. If your performance results are lin

[gmx-users] ngmx not installed in gmx4.6.1

Dear gmx users, I had installed gromacs 4.6.1 using cmake. All the binaries are installed, but surprisingly I do not find ngmx executable. Can anyone guide me how do I install ngmx using cmake. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] pullx file content with pull_geometry = position

Dear gromacs user, I run a simulation where I restrain two groups in a specific position with respect to one another: one is part of a protein (index group name: pull_group) the other is just one ion (index pull_group name r_60022). I have the following parameters in my mdp file:

Re: [gmx-users] Re: gmx 4.6 mpi installation through openmpi?

Compile and install your own FFTW per the install guide? At least that eliminates a variable. Mark On Tue, Jun 4, 2013 at 2:53 PM, escajarro wrote: > I received this answer: > > Mark Abraham Mon, 03 Jun 2013 08:02:56 -0700 > > That looks like there's a PGI compiler getting used at some point (

Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q

On Tue, Jun 4, 2013 at 4:50 PM, Jianguo Li wrote: > > > Thank you, Mark and Xavier. > > The thing is that the cluster manager set the > minimum number of cores of each jobs in Bluegene/Q is 128, so I can not > use 64 cores. But according to the performance, 512 cores in Bluegene > roughly equival

Re: [gmx-users] About coulmb & Vanderrwalls cutoff

On 6/4/13 11:25 AM, vidhya sankar wrote: Dear Justin Thank you for yoyr Previuos reply I am using Gromos96 53a6 so i am using the following parameters ns_type = grid nstlist = 5 rlist = 0.9 rcoulomb= 0.9 rvdw

[gmx-users] About coulmb & Vanderrwalls cutoff

Dear Justin Thank you for yoyr Previuos reply     I am using  Gromos96 53a6  so i am using  the following parameters ns_type = grid   nstlist = 5   rlist   = 0.9 rcoulomb    = 0.9 

Re: [gmx-users] Can we connect two boxes together for the simulation?

On 6/4/13 10:12 AM, Bao Kai wrote: Hi, I guess the renumbering of the atoms and molecules will be a problem, especially when the two boxes contain the same type of the molecules. How can we handle that? genconf -renumber -Justin -- Justin A. Le

Re: [gmx-users] how to add sodium acetate

On 6/4/13 10:05 AM, maggin wrote: Hi, when we add Nacl, can use -pname NA -nname cl in GMX so for sodium acetate, how to display it ? Use genbox -ci -nmol to add the acetate molecules, then genion to add Na+ ions. -Justin -- Justin A. Lemkul, Ph.D

Re: [gmx-users] Can we connect two boxes together for the simulation?

On 6/4/13 8:46 AM, Bao Kai wrote: Hi, all, I want to do NPT simulations with different compositions first. Then I want to connect the two boxes to continue the NPT simulation. I mean, after simulations, we get two boxes with different compositions. Can we do that with gromacs? or how can we

Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q

Thank you, Mark and Xavier. The thing is that the cluster manager set the minimum number of cores of each jobs in Bluegene/Q is 128, so I can not use 64 cores. But according to the performance, 512 cores in Bluegene roughly equivalent to 64 cores in another cluster. Since there are 16 cores

Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q

Thank you XAvie. The thing is that the cluster manager set the minimum number of cores of each jobs in Bluegene/Q is 128, so I can not use 64 cores. But according to the performance, 512 cores in Bluegene roughly equivalent to 64 cores in another cluster. Since there are 16 cores in each comput

Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q

On Tue, Jun 4, 2013 at 4:20 PM, XAvier Periole wrote: > > BG CPUs are generally much slower (clock whose) but scale better. > > You should try to run on 64 CPUs on the Blue gene too for faire comparison. > The number of CPUs per nodes is also an important factor: the more CPUs > per nodes the mor

Re: [gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q

BG CPUs are generally much slower (clock whose) but scale better. You should try to run on 64 CPUs on the Blue gene too for faire comparison. The number of CPUs per nodes is also an important factor: the more CPUs per nodes the more communications needs to be done. I observed a significant slow

[gmx-users] Can we connect two boxes together for the simulation?

Hi, I guess the renumbering of the atoms and molecules will be a problem, especially when the two boxes contain the same type of the molecules. How can we handle that? Thanks. Best, Kai editconf is a nice tool to create vacuum in your box. You can then insert one of your box into anoth

Re: [gmx-users] Can we connect two boxes together for the simulation?

editconf is a nice tool to create vacuum in your box. You can then insert one of your box into another box using cat box1.gro box2.gro, just remove the very last line in box1.gro. Dr. Vitaly Chaban On Tue, Jun 4, 2013 at 2:46 PM, Bao Kai wrote: > Hi, all, > > I want to do NPT simulation

[gmx-users] how to add sodium acetate

Hi, when we add Nacl, can use -pname NA -nname cl in GMX so for sodium acetate, how to display it ? Thank you very much! maggin -- View this message in context: http://gromacs.5086.x6.nabble.com/how-to-add-sodium-acetate-tp5008786.html Sent from the GROMACS Users Forum mailing list archive

[gmx-users] Performance of Gromacs-4.6.1 on BlueGene/Q

Dear All, Has anyone has Gromacs benchmark on Bluegene/Q? I recently installed gromacs-461 on BG/Q using the following command: cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \   -DGMX_BUILD_OWN_FFTW=ON \ -DBUILD_SHARED_LIBS=OFF \ -DGMX_XML=OFF \ -DCMAKE

[gmx-users] Running gmx-4.6.x over multiple homogeneous nodes with GPU acceleration

Dear all, Since gmx-4.6 came out, I've been particularly interested in taking advantage of the native GPU acceleration for my simulations. Luckily, I have access to a cluster with the following specs PER NODE: CPU 2 E5-2650 (2.0 Ghz, 8-core) GPU 2 Nvidia K20 I've become quite familiar with the

[gmx-users] Re: gmx 4.6 mpi installation through openmpi?

I received this answer: Mark Abraham Mon, 03 Jun 2013 08:02:56 -0700 That looks like there's a PGI compiler getting used at some point (perhaps the internal FFTW build is picking up the CC environment var? I forget how that gets its compiler!). If you do find * -name config.log then perhaps you c

[gmx-users] Can we connect two boxes together for the simulation?

Hi, all, I want to do NPT simulations with different compositions first. Then I want to connect the two boxes to continue the NPT simulation. I mean, after simulations, we get two boxes with different compositions. Can we do that with gromacs? or how can we do that? Thanks. Best, Kai -- gmx-u

Re: [gmx-users] About Physical parameters

On 6/4/13 8:22 AM, vidhya sankar wrote: Dear Justin Thank you for your Previuos reply I am using gromos53a6 ff When i changed the parameters for cut-off (r list ) value to 1.2 I have got Error as follows Wh

[gmx-users] About Physical parameters

Dear Justin Thank you for your Previuos reply     I am using gromos53a6 ff When i changed the parameters for cut-off  (r list ) value to 1.2 I have got Error as follows  What is the Meaning of Note 2 & 3 NOTE 2 [fi

Re: [gmx-users] High Initial generated Temp

On 6/4/13 8:07 AM, tarak karmakar wrote: Dear All, Although I have set gen_temp = 300, it is showing the initial temperature 445.7 K, generated at the very beginning of the run. gen_vel = yes ; velocity generation gen_temp= 300 gen_seed

[gmx-users] High Initial generated Temp

Dear All, Although I have set gen_temp = 300, it is showing the initial temperature 445.7 K, generated at the very beginning of the run. gen_vel = yes ; velocity generation gen_temp= 300 gen_seed= 93873959697 Is it because of a bad geo

Re: [gmx-users] problem using g_lie

On 6/4/13 3:56 AM, khushboo bafna wrote: hii I ran a protein ligand simulation and only ligand simualtion in water using GROMACS 4.5.4 I want to find the binding energy of the ligand and used g_lie. I tried to run g_lie on ligand simulation in water and got the following result Opened md_1.e

Re: [gmx-users] About Physaica Parameter

On 6/4/13 5:06 AM, vidhya sankar wrote: Dear Justin & Mark Thank you for your previous reply I am doing Simulation of CNT wrapped By Cyclic Peptide in Water For that I have used the Parameters as follows for my prod

[gmx-users] REMD run showing temperature range more than the equilibrated.

Hi all ! well, I'm working on REMD with 96 replicas, with temperature range 280K to 425.04K. The NVT equilibration works well and graphs plotted show almost the required temperature after equilibration. Then, after 3 ns of remd run , the edr -> xvg files show initial temperature atleast 40 -50 u

Re: [gmx-users] GPU problem

Hi Albert, I think using -nt flag (-nt=16) with mdrun would solve your problem. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Jun 4, 2013 at 12:56 PM, Albert wrote: > Dear: > > I've got four GPU in one workstation. I am trying to run two GPU job with > command: > > mdrun -s md

[gmx-users] About Physaica Parameter

Dear Justin & Mark Thank you for your previous reply       I am doing Simulation of CNT wrapped By Cyclic Peptide in Water For that I have used the Parameters as follows for my production run ns_type        = grid       nstl

[gmx-users] problem using g_lie

hii I ran a protein ligand simulation and only ligand simualtion in water using GROMACS 4.5.4 I want to find the binding energy of the ligand and used g_lie. I tried to run g_lie on ligand simulation in water and got the following result Opened md_1.edr as single precision energy file Using the

[gmx-users] GPU problem

Dear: I've got four GPU in one workstation. I am trying to run two GPU job with command: mdrun -s md.tpr -gpu_id 01 mdrun -s md.tpr -gpu_id 23 there are 32 CPU in this workstation. I found that each job trying to use the whole CPU, and there are 64 sub job when these two GPU mdrun submitte