Re: [gmx-users] Installation Problem... No command 'gmx' found

Hi, Try gmx_mpi. Regards Terry > On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir > wrote: > > Dear all user > > I install gromacs in my laptop its perfectly ok. But i have problem to > install in my desktop there i face problem. > In my desktop i want to

[gmx-users] Installation Problem... No command 'gmx' found

Dear all user I install gromacs in my laptop its perfectly ok. But i have problem to install in my desktop there i face problem. In my desktop i want to compile with cuda accelerator and MPI option. I install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all this driver is ok. For

Re: [gmx-users] sugar puckering

Dear Gmx Users, I am interested in calculating cremer-pople parameters for a trisachharide ligand from its simulation docked with a protein. I found one tool g_puckering for calculating the parameters but it was written for Gromacs version 4.0.x and I am using version 5.0.4. I am not able to

Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU

Hi, Can you also explain why the function calls to cudaDriverGetVersion() and cudaRuntimeGetVersion() both return 0, as in >> CUDA driver:0.0 >> CUDA runtime: 0.0 Thanks, Tim At 2016-04-21 08:49:17, "Szilárd Páll" wrote: >On Thu, Apr 21, 2016 at 12:22 AM,

Re: [gmx-users] mdrun on multiple nodes

On Thu, Apr 21, 2016 at 2:20 AM, Husen R wrote: > Hi, > > > Thank a lot for the information. > > in my gromacs installation, 'gmx_mpi' is works while 'mdrun_mpi' is not > recognized as a gromacs command. Just as expected; the binary is suffixed, not the comand and you built a

Re: [gmx-users] gromacs 5.1.2 mdrun can't detect GPU

On Thu, Apr 21, 2016 at 12:22 AM, treinz wrote: > Hi all, > > > I recently built 5.1.2 with GPU support and the config options are: > > > module load cuda/7.5.18 > cmake .. -DCMAKE_C_COMPILER=gcc-4.9 \ > -DCMAKE_CXX_COMPILER=g++-4.9 \ > -DGMX_MPI=OFF \ >

Re: [gmx-users] mdrun on multiple nodes

Hi, Thank a lot for the information. in my gromacs installation, 'gmx_mpi' is works while 'mdrun_mpi' is not recognized as a gromacs command. Regards, Husen On Wed, Apr 20, 2016 at 6:42 PM, Mark Abraham wrote: > Hi, > > Well spotted. These should all be along

[gmx-users] gromacs 5.1.2 mdrun can't detect GPU

Hi all, I recently built 5.1.2 with GPU support and the config options are: module load cuda/7.5.18 cmake .. -DCMAKE_C_COMPILER=gcc-4.9 \ -DCMAKE_CXX_COMPILER=g++-4.9 \ -DGMX_MPI=OFF \ -DGMX_THREAD_MPI=ON \ -DGMX_GPU=ON \

Re: [gmx-users] Long distance effects of mutation and stability

I forgot to mention, I may also do simulations with the complex, mutated protein + partner, again addressing the same questions. Will 100 ns be enough, even for the larger complex? In general, how can I know if the simulation time is enough, that I am not missing modes of motion? On Wed, Apr 20,

[gmx-users] trouble with ca2+ atom and SEP recognition in Gromacs 5.1.1

Hi! All I have been running into some trouble with CA2+ recognition in GMX 5.1.1. So some back ground..I have a protein that I am trying to simulate that has three chains.First chain is 161 amino acids long, second one is about 200AA and the third one is about 280 AA long. They have their

[gmx-users] Long distance effects of mutation and stability

I want to analyse the effects of a point mutation in a protein. The protein is 150 amino acids long. I have experimental evidence that a mutation has a distant effect in the protein. More precisely, the mutation affects the binding of the protein to another partner, even though the mutation

Re: [gmx-users] atomtypes

Do you know please any source for them by chance? The best, On Wed, Apr 20, 2016 at 8:03 PM, Justin Lemkul wrote: > > > On 4/20/16 2:01 PM, Alexander Alexander wrote: > >> Thanks. >> Then no matter which program or package has been used to drive them? then >> I >> can take them

Re: [gmx-users] atomtypes

On 4/20/16 2:01 PM, Alexander Alexander wrote: Thanks. Then no matter which program or package has been used to drive them? then I can take them and use in Gromacs. A force field is a force field, as long as the functional form is supported by GROMACS you can use it. Also, No matter if

Re: [gmx-users] atomtypes

Thanks. Then no matter which program or package has been used to drive them? then I can take them and use in Gromacs. Also, No matter if they have been derived for a bulk crystal of the element or its surface or even a complex molecule? Cheers, Alex On Wed, Apr 20, 2016 at 7:52 PM, Justin Lemkul

[gmx-users] vdwradii issue

Dear Gmx-Users Currently i'm having this kind of sticky warning when i am doing gmx solvate or gmx editconf (ff was charmm and oplsa). However i copied vdwradii.dat in my working directory, or use -vdwread flag still get this warning..Please how to get rid off of this Warning!    WARNING:

Re: [gmx-users] atomtypes

On 4/20/16 1:50 PM, Alexander Alexander wrote: Dear GMXuser, Suppose I have the *.gro file for the (111) surface of for example Ni or Pt or Au, then, I was wondering that where I can find the required information in [ atomtypes ] section for this surface, especially sigma and epsilon? [

[gmx-users] atomtypes

Dear GMXuser, Suppose I have the *.gro file for the (111) surface of for example Ni or Pt or Au, then, I was wondering that where I can find the required information in [ atomtypes ] section for this surface, especially sigma and epsilon? [ atomtypes ] ; name masschargeptype

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

On 4/20/16 1:20 PM, Tuhin Samanta wrote: I have done the energy minimization many times by taking previously minimized structure. A box of water should be basically impossible to break. Either your .mdp or topology has problems. Since you've provided neither, there's not much anyone can

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

That's just the first stage of an equilibration. See http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation for suggestions Mark On Wed, 20 Apr 2016 19:20 Tuhin Samanta wrote: > I have done the energy minimization many times by taking previously

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

I have done the energy minimization many times by taking previously minimized structure. On Wed, Apr 20, 2016 at 10:39 PM, Mark Abraham wrote: > Hi, > > On Wed, 20 Apr 2016 19:04 Tuhin Samanta > wrote: > > > Thank Mark for your

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

Hi, On Wed, 20 Apr 2016 19:04 Tuhin Samanta wrote: > Thank Mark for your suggestion. > > I was trying to resolve the problem > " 4 particles communicated to PME node 4 are more than 2/3 times the > cut-off out of the domain decomposition cell of their charge

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

Thank Mark for your suggestion. I was trying to resolve the problem " 4 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated."

Re: [gmx-users] gmx covar: Segmentation fault

On 4/20/16 10:57 AM, Oliwia Maria Szklarczyk wrote: Why is it reading one frame more than the last frame number?… Could that be a bug? No. Trajectories include t=0, so there's always one more frame than you might expect. The "last frame" is based on index (starting from zero), IIRC.

[gmx-users] gmx covar: Segmentation fault

> Dear All, > > Anyone has experience with the covariance analysis program from gromacs? I > can’t get rid of the segmentation fault. I run the following: > > gmx covar -f md.xtc -s md.tpr -v eigenvec.trr -n sys.ndx > > And this is the output: > > Choose a group for the least squares fit >

Re: [gmx-users] gmx covar: Segmentation fault

Why is it reading one frame more than the last frame number?… Could that be a bug? > On 20 Apr 2016, at 16:51, Oliwia Maria Szklarczyk wrote: > > Dear All, > > Anyone has experience with the covariance analysis program from gromacs? I > can’t get rid of the segmentation

[gmx-users] gmx covar: Segmentation fault

Dear All, Anyone has experience with the covariance analysis program from gromacs? I can’t get rid of the segmentation fault. I run the following: gmx covar -f md.xtc -s md.tpr -v eigenvec.trr -n sys.ndx And this is the output: Choose a group for the least squares fit Group 0 (

Re: [gmx-users] on md of protein-ligand

Dear Justin, Then there should be multiple ligand gro files pasted onto the single protein complex gro file, right? Brett At 2016-04-20 17:45:50, "Justin Lemkul" wrote: > > >On 4/20/16 5:21 AM, Brett wrote: >> Hi Mark, >> >> >> >> I still find it was difficult to

Re: [gmx-users] on md of protein-ligand

On 4/20/16 9:26 AM, Brett wrote: Dear Justin, Then there should be multiple ligand gro files pasted onto the single protein complex gro file, right? Whatever you want to simulate has to be present. -Justin Brett At 2016-04-20 17:45:50, "Justin Lemkul"

Re: [gmx-users] Analysis of trajectory form Gromacs 5.1.2. in Gromacs 5.0.4

Thank you Justin for your quick reply. Like you suggested, I built a new .tpr file with 5.0.4 and everything worked fine. Melanie Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se im Auftrag von

[gmx-users] H6 DPOPG problem

Dear gromacs users, I'm trying to run a simulation using a preequilibrated membrane. everything looks fine until I try to run an energy minimization. Apparently there is an energy clump so EM stops after some steps without reaching the requested Fmax. The problem seems to involve the H6 atoms of

Re: [gmx-users] Remove bad waters

Hi, If you've done that properly, then you will have some holes in your membrane and will need to re-equilibrate, e.g. Doing EM and theN perhaps using a small time step while the local unhappiness resolves gently. Mark On Wed, 20 Apr 2016 14:01 Mehrnoosh Hazrati

Re: [gmx-users] Remove bad waters

Thank you dear Mark. actually when I change my gro file by text and remove those water molecules, I got "cannot settle water molecule" error, that I didn't get using the first gro file. So that I thought this way may not be appropriate! Indeed, I don't get any error with those water molecules

Re: [gmx-users] Remove bad waters

Hi, This is easy to do in a text editor, because the z coordinates will stand out from the others. Make sure you also adjust the numbers of atoms and molecules accordingly. But a little bit of diffusion of water into the membrane can be physical (I think!) but too much suggests your model is

Re: [gmx-users] mdrun on multiple nodes

Hi, Well spotted. These should all be along the lines of mpirun -np 2 gmx_mpi mdrun or mpirun -np 2 mdrun_mpi if the admins have done an mdrun-only installation. I'll fix that for future versions Mark On Wed, 20 Apr 2016 13:34 Husen R wrote: > Hi Mark, > > I'm wondering

Re: [gmx-users] mdrun on multiple nodes

Hi Mark, I'm wondering why in this link http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html 'gmx' is used to run mdrun on more than one node instead of 'gmx_mpi' ? Regards, Husen On Wed, Apr 20, 2016 at 3:48 PM, Mark Abraham wrote: > Hi,

Re: [gmx-users] Analysis of trajectory form Gromacs 5.1.2. in Gromacs 5.0.4

On 4/20/16 7:25 AM, König, Melanie wrote: Dear all, I ran the MD simulation of my system on a cluster using the new Gromacs version 5.1.2. I want to analyse the trajectory on my computer with Gromacs tools from version 5.0.4. No matter which tool I use, a problem occurs. Gromacs tries

[gmx-users] Analysis of trajectory form Gromacs 5.1.2. in Gromacs 5.0.4

Dear all, I ran the MD simulation of my system on a cluster using the new Gromacs version 5.1.2. I want to analyse the trajectory on my computer with Gromacs tools from version 5.0.4. No matter which tool I use, a problem occurs. Gromacs tries to read the md.tpr file but gives an error

Re: [gmx-users] Zn moves away from protein - ligand complex

Hi Mark, I got you now. Thanks for your kind reply. Best wish :D Hongtham On Wed, Apr 20, 2016 at 4:19 AM, Mark Abraham wrote: > Hi, > > You've already said you know the ion isn't diffusing out, so there can be > no simulation problem. > > You'd have the same kind of

Re: [gmx-users] mdrun on multiple nodes

Hi Mark, I have configured gromacs with mpi support (using -DGMX_MPI=on): tar xfz gromacs-5.1.2.tar.gz cd gromacs-5.1.2 mkdir build cd build cmake .. -DGMX_MPI=on -DGMX_BUILD_OWN_FFTW=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Currently, I tried to use gmx_mpi (as

Re: [gmx-users] mdrun on multiple nodes

Hi Mark, I have configured gromacs with mpi support (using -DGMX_MPI=on): tar xfz gromacs-5.1.2.tar.gz cd gromacs-5.1.2 mkdir build cd build cmake .. -DGMX=on -DGMX_BUILD_OWN_FFTW=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC Currently, I tried to use gmx_mpi (as you

Re: [gmx-users] on md of protein-ligand

Hi, On Wed, Apr 20, 2016 at 11:21 AM Brett wrote: > Hi Mark, > > > > I still find it was difficult to understand. After the pdb2gmx, the > coordinates in the gro file will be significantly (including the scale of > the value) different from the input for pdb2gmx. Suppose my

Re: [gmx-users] (no subject)

On 4/20/16 2:51 AM, Terry wrote: Hi, The mailing list doesn't allow attachment. Try another method to share your file. Gromacs is complaining the file "forcefield.itp", not "lig.itp". So my guess is you have a corrupted file. Or the sequence of #include statements in the .top is wrong.

Re: [gmx-users] disulfate bond between 2 chains

On 4/20/16 5:20 AM, Ming Tang wrote: Dear list, Is there anybody who generated the disulfate bonds between 2 different chains? I used -chainsep but did not get what I want. If I choose -chainsep interactive (n), it will generate the disulfate bond between 2 chains (only after enlarge the

Re: [gmx-users] on md of protein-ligand

On 4/20/16 5:21 AM, Brett wrote: Hi Mark, I still find it was difficult to understand. After the pdb2gmx, the coordinates in the gro file will be significantly (including the scale of the value) different from the input for pdb2gmx. Suppose my protein-ligand contains 6 identical ligands,

Re: [gmx-users] on md of protein-ligand

Hi Mark, I still find it was difficult to understand. After the pdb2gmx, the coordinates in the gro file will be significantly (including the scale of the value) different from the input for pdb2gmx. Suppose my protein-ligand contains 6 identical ligands, the ATB like servers can only

Re: [gmx-users] MARTINI simulation of protein-protein recognition

Yes actually I did this but by hands which was not very comfortable :-) Hope that martini developers will add possibility to make such kind of systems more trivially :-) J. 2016-04-19 17:11 GMT+02:00 : > ok shouldn't martinize do the equivalent to pdb2gmx, i.e. make

[gmx-users] Heat capacity Cv

Dear Gromacs user, In order to get heat capacity for a solid, I do a long and well converged mini-NPT-NVT simulations and then invoke below command to get Cv; gmx energy -f nvt.edr -nmol 8192 -fluct_props -driftcorr -b 500 -o cv.xvg However, Cv comes always to "24.5815 J/mol K" for different

Re: [gmx-users] on md of protein-ligand

Hi, The topology and the coordinates are two separate sets of infomation. You already expect that lot of conformations will be consistent with the topology, and explored over the simulations. The topology generating servers want a structure so they can make good chemical guesses for you. But

Re: [gmx-users] problem regarding cut-off and the PME grid spacing

Hi, The information message and the actual error are separated in your log file with a bunch of punctuation because they're logically separate. Anyway, there should also have been a link to http://www.gromacs.org/Documentation/Errors which suggests some strategies for this issue. Mark On Wed,

Re: [gmx-users] mdrun on multiple nodes

Hi, Probably you haven't built gromacs with MPI support, else the name of the binary would be gmx_mpi. You can get that confirmed if you look further down the output .log files. Mark On Wed, 20 Apr 2016 10:09 Husen R wrote: > Hi all, > > I tried to run mdrun on more than one

[gmx-users] mdrun on multiple nodes

Hi all, I tried to run mdrun on more than one node using the command available in this url http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-performance.html . The following is my sbatch job : ###SBATCH #!/bin/bash #SBATCH -J sim #SBATCH -o

[gmx-users] on md of protein-ligand

Dear All and Justin, Suppose my protein complex contain 4 ADP, each ADP was in one subunit. Suppose we use ATB to create the ligand ADP files for md. It seems the situation is, regardless of which of the 4 ADP pdb files was submitted, ATB will only give one identical set of topology files for

Re: [gmx-users] protein ligand simulation

On Wed, Apr 20, 2016 at 10:27 AM, Justin Lemkul wrote: > [image: Boxbe] This message is eligible > for Automatic Cleanup! (jalem...@vt.edu) Add cleanup rule >

[gmx-users] problem regarding cut-off and the PME grid spacing

Hello , My system involves water molecules in a box of 5x5x5 nm3. When I was doing the simulation for energy minimization I got n error message -- The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher

Re: [gmx-users] (no subject)

Hi, The mailing list doesn't allow attachment. Try another method to share your file. Gromacs is complaining the file "forcefield.itp", not "lig.itp". So my guess is you have a corrupted file. Terry On Wed, Apr 20, 2016 at 2:42 PM, Uma Devi wrote: > i am running protein

[gmx-users] (no subject)

i am running protein with ligand complex. i am following the methods given by justin. i am using opls force field. i have converted the protein pdb using pdb2gmx and ligand file using topolgen. after that i have concatenated both in gro and include the lig.itp in topology file. while performing