[gmx-users] how to generate tng format trajectory?

Hello all, I just learned that the tng trajectory format file is even more smaller than the .xtc format file. I am just wondering how shall we specify the option in the .mdp file so that "gmx mdrun" could generate the .tng format trajectory accordingly? thanks a lot albert

Re: [gmx-users] Center of mass motion removal

I also frequently encounter this headache problem. Is it possible to center the protein in the pbc box during simulation? As far as I know Desmond has a function to do this, so that we don't need to do anything else to recenter our protein in the box. Albert On 12/13/2019 11:51 PM, Alex

[gmx-users] problem of MD simulation

Hello, I have compiled my Gromacs 2019v3 with the following command line in a GPU workstation: env CC=mpicc CXX=mpicxx F77=mpif90 FC=mpif90 LDF90=mpif90 cmake .. -DCMAKE_INSTALL_PREFIX=/soft/gromacs/2019v3-intel -DGMX_MPI=ON -DGMX_GPU=ON -DGMX_PREFER_STATIC_LIBS=O I try to run my MD with

Re: [gmx-users] strange structure after energy minimization

Dear Justin, Thanks a lot for your information. Can we do something in Gromacs to prevent this happen? Building 50 aa for a disorder section is very challenging which may result in too many artifices. thanks a lot Albert On Sun, Oct 27, 2019 at 1:52 PM Justin Lemkul wrote: > > > On

[gmx-users] strange structure after energy minimization

Hello, I've performed a energy minimization in Gromacs 2018v4. The structure looked very strange after energy minimization: There is a big gap in the structure for residue 400-450, which is missing in the initial crystal structure. After energy minimization, gromacs connected residue 399 to 451

[gmx-users] slow gmx

15.0 seconds: Connection timed out Does anybody know hot to resolve this problem? Thanks a lot Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support

Re: [gmx-users] Workstation choice

May I ask how many atoms in the system? Which forcefield did you use? And what's the time step? regards On 09/10/2018 09:14 PM, Olga Selyutina wrote: (50 ts instead of 5000 ts, otherwise it's too fast) That would be a factor of about 227! On an available machine (not used for

Re: [gmx-users] Qm/mm

why not try some professional QM/MM software like "ORCA". It will make your life much easier. On 08/24/2018 11:54 PM, rose rahmani wrote: Hi, I want to use qm/mm calculations(dfb3 code & ONIOM method) in gromacs. Since, some of these codes are commercial(like ONIOM specially Gaussian), i

Re: [gmx-users] Excessive and gradually increasing memory usage with OpenCL

probably link to http://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html, which clarifies that even the latest release of CUDA does not come close to being compatible with the latest version of GCC. -Albert Mao On Tue, Mar 27, 2018 at 4:43 PM, Szilárd Páll <pall.szil...@gmail.com>

[gmx-users] Excessive and gradually increasing memory usage with OpenCL

of a sad problem where building with CUDA support fails due to the C compiler being "too new". Thanks! -Albert Mao GROMACS: gmx mdrun, version 2018 Executable: /data/albertmaolab/software/gromacs/bin/gmx Data prefix: /data/albertmaolab/software/gromacs Command line: gmx mdrun

Re: [gmx-users] how to restrain secondary structure?

Oh, my I thought Gromacs is smart enough to provide this function using some command line On 11/25/2017 09:17 PM, Justin Lemkul wrote: You have to write the restraints by hand or create a script that will do it for you. genrestr is not smart enough to do such things. -Justin

Re: [gmx-users] how to restrain secondary structure?

thank you for the reply. May I ask which command should I use? I checked, gmx_mpi genrestr but I cannot find the option you mentioned. thanks a lot. On 11/25/2017 09:02 PM, Justin Lemkul wrote: Apply [dihedral_restraints] to the phi and psi torsions you want to restrain. -Justin --

[gmx-users] how to restrain secondary structure?

Hello, I would like to add a small force constant to the backbone of a-helix and b-strand. I am just wondering how can we do this in Gromacs? thanks a lot Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] overlapped parameters

Hello, I have set my topol.top file as following: ; Include forcefield parameters #include "charmm36-jul2017.ff/forcefield.itp" #include "input/unk.prm" #include "input/unk.itp" Then I run grompp command line. I obtained the following warnings: WARNING 1 [file unk.prm, line 22]:   Overriding

Re: [gmx-users] CgenFF conversion failed

file sent to you private email address. thx a lot On 11/19/2017 06:06 PM, Justin Lemkul wrote: On 11/19/17 11:34 AM, Albert wrote: Hello, I generated a ligand.str file from Parachem website. Then, I try to convert it to Gromacs format with command line: >cgenff_charmm2gmx.py

[gmx-users] CgenFF conversion failed

doc : 4.0 NOTE3: In order to avoid duplicated parameters, do NOT select the 'Include parameters that are already in CGenFF' option when uploading a molecule into CGenFF. Traceback (most recent call last): File "/home/albert/bin/cgenff_charmm2gmx.py", line 799, in m.read_charmm

[gmx-users] possible bug in convert-tpr

l list to make sense of it all. Many thanks, Albert P. S. - I just attached the most basic files to reproduce the bug. I could attach more, but that would exceed the 50K limit that the list imposes. In any case, the rest of the files can be found in the VOTCA email thread,

[gmx-users] problem of GB simulation

% step 144300, remaining wall clock time: 207 s vol -0.00! imb F 23% step 144400, remaining wall clock time: 207 s --- Program gmx mdrun, VERSION 5.1.4 Source code file: /icm/home/albert/tmp/gromacs-5.1.4/src/gromacs/mdlib/nsgrid.c, line: 633

[gmx-users] QM/MM in Gromacs-5.1.4?

Hello, I would like to use ORCA as a QM engine for Gromacs QM/MM simulation. I am just wondering shall we add additional options to cmake when we compile Gromacs? Thanks a lot Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] GPU job failed

/albert/Downloads/gromacs/gromacs-5.1.3/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu, line: 403 Fatal error: cudaCreateTextureObject on nbfp_texobj failed: invalid argument For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org

Re: [gmx-users] multiple cpu for g_membed job?

oh, I see. thx a lot On 07/31/2017 04:48 PM, Mark Abraham wrote: Hi, Only one rank, but I believe it works with the Verlet scheme and thus openmp and a single GPU. Mark -- Gromacs Users mailing list * Please search the archive at

[gmx-users] multiple cpu for g_membed job?

Hi guys, Does anybody know whether g_membed support parallel running using multiple CPU for a single job? thanks a lot Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http

[gmx-users] PBC problem

The issue is still there. Here is a snapshot for my problem: https://www.dropbox.com/s/qvoxa70tr625w46/pbc.jpg?dl=0 Does anybody have any idea how to solve this problem? Thank you very much. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

[gmx-users] offline version of CgenFF tool?

Hello, does anybody have any idea is there any offline tool for generating CgenFF parameters for a ligand? Currently I have to go to cgenff website to generate. It is very inconvenient if we have a vast number of ligand. Thanks a lot Albert -- Gromacs Users mailing list * Please search

Re: [gmx-users] g_membed in 5.1.4?

Hi guys thanks a lot for helpful suggestions. Finally it works. cheers. ^_^ On 01/29/2017 03:18 PM, Mark Abraham wrote: Specifically http://manual.gromacs.org/documentation/2016.1/user-guide/mdrun-features.html#running-a-membrane-protein-embedding-simulation Mark -- Gromacs Users mailing

Re: [gmx-users] g_membed in 5.1.4?

Unfortunately I didn't find anything about what's ".dat" should be, what's the format. The option -membed does what used to be g_membed, i.e. embed a protein into a membrane. This module requires a number of settings that are provided in a data file that is the argument of this option. For

Re: [gmx-users] g_membed in 5.1.4?

It seems to work. However, I find that it probably quite different from the old one in 4.x. It asked us to problem a .dat file. -membed [<.dat>] (membed.dat) (Opt.) Generic data file I am just wondering what kind of .dat file shall we provide? Is there any example?

[gmx-users] domain decomposition problems

in all. Does anybody have other suggestions? Thanks a lot. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests

Re: [gmx-users] g_membed in 5.1.4?

It doesn't work in 5.1.4: >gmx_mpi membed -h --- Program: gmx_mpi, VERSION 5.1.4 Source file: src/gromacs/commandline/cmdlinemodulemanager.cpp (line 376) Function:gmx::CommandLineModuleInterface*

[gmx-users] g_membed in 5.1.4?

Hello, I would like to build a membrane system with the g_membed tool in Gromacs. However, I cannot find it in 5.1.4. I am just wondering is it still available in the new version? Thanks a lot Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

[gmx-users] Gromacs in Xeon Phi?

Hello: Does anybody have any idea how fast Gromacs it is in a Intel Xeon Phi machine? Is it comparable with normal Xeon CPU or GTX 1080/GTX 980Ti GPU? My typical simulation system is: 50-60 K atoms, CHARMM36 FF, NPT ensemble for MD production, 2fs time step. Thanks a lot Albert

Re: [gmx-users] about potential energy calculation

noprobably that's the reason? On 01/13/2017 12:23 PM, Anders Støttrup Larsen wrote: Do you have the same amount of molecules in each simulation? Anders -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] about potential energy calculation

Hello: I submitted MD simulation for two small peptides with Amber FF. I calculated the average potential energy of the system: peptide A: -9x10^4 kcal/mol peptide B: -6X10^4 kcal/mol it seems that peptide A is more stable than B. However, if I extract each frame the peptide from MD

[gmx-users] which version would be faster?

with both GPUs and there are around 60'000 atom in the system. Thank you very much. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] CPU running doesn't match command line

I use command line "top" to check how many CPUs are using. Each gmx occupied 7.5 CPU. On 08/23/2016 06:38 PM, Mark Abraham wrote: Hi, How did you decide that only 15 cores were being used? What performance did you observe with only one of the jobs running, vs the performance of both of

[gmx-users] water cluster

Hello: I finished a MD simulation and I am interested in the water occupancy in a specific region. I am just wondering is there any tool in Gromacs could do this? Would g_cluster or calculation on average structure would be helpful? Thank you very much. Albert -- Gromacs Users mailing list

Re: [gmx-users] CPU running doesn't match command line

Hello Mark: I've recompiled Gromacs without MPI. I run submit the job with the command line you suggested. gmx mdrun -ntomp 10 -v -g test.log -pin on -pinoffset 0 -gpu_id 0 -s test.tpr >& test.info gmx mdrun -ntomp 10 -v -g test.log -pin on -pinoffset 10 -gpu_id 1 -s test.tpr >& test.info

Re: [gmx-users] about position restrain

Hi Justin, thanks for the advice. The are plenty of paper have discussed that it is necessary to restrain the backbone ,or at lease the CA atoms, of a homology models. Otherwise it would turn out to be something completely nonsense. Probably restrain the secondary structure would be

[gmx-users] about position restrain

spontaneously. According to my experiences, if we add position restrain to the protein backbone, probably the overall protein will stay in the same place forever. It won't drift to somewhere else. I am just wondering what we can do? Thank you very much Albert -- Gromacs Users mailing list * Please

Re: [gmx-users] CPU running doesn't match command line

anybody has more suggestions? thx a lot On 08/17/2016 09:07 AM, Albert wrote: Hello: Here is the information that you asked for. gmx_mpi mdrun -s 7.tpr -v -g 7.log -c 7.gro -x 7.xtc -ntomp 8 -gpu_id 0 -pin

Re: [gmx-users] CPU running doesn't match command line

: enabled C++11 compilation: disabled TNG support:enabled Tracing support:disabled Built on: Thu Aug 11 16:15:26 CEST 2016 Built by: albert@cudaB [CMAKE] Build OS/arch: Linux 3.16.7-35-desktop x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R

Re: [gmx-users] CPU running doesn't match command line

Hello: Here is my MDP file: define = -DREST_ON -DSTEP6_4 integrator = md dt = 0.002 nsteps = 100 nstlog = 1000 nstxout = 0 nstvout = 0 nstfout = 0

Re: [gmx-users] CPU running doesn't match command line

Hello: I add additional option to one of the job: -pinoffset 8 to the command line. But it is still the same.However, if I remove option "-pin on" from one of the job, 16 CPU were occupied On 08/16/2016 04:18 PM, Szilárd Páll wrote: By starting two (piined) runs without an

[gmx-users] CPU running doesn't match command line

you very much. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/ma

Re: [gmx-users] job suspended in local workstation

there is no any errors messages if I run it from terminal for a specific step Everything goes well On 08/12/2016 03:46 PM, Mark Abraham wrote: Hi, Run job.whateveritis and see the error message. Mark -- Gromacs Users mailing list * Please search the archive at

[gmx-users] job suspended in local workstation

Hello: I wrote all steps for Gromacs MD simulation in a .tcsh script. Then I submitted the job into the local GPU workstation by command line: nohup ./job.tcsh & However, I obtained the following messages immediately: nohup ./job.csh & [1] 13433 No any steps is running after I submit the

Re: [gmx-users] MPI GPU job failed

I just found that I compiled PLumed plugin with a different MPI, and then patched Gromacs. Now, I recompiled everything from scratch, finally it works. thx a lot On 08/11/2016 05:55 PM, Szilárd Páll wrote: It should. You can always verify it in the header of the log file. It's always useful

Re: [gmx-users] MPI GPU job failed

-s 62.tpr -gpu_id 01 It stilled failed. --- Program gmx mdrun, VERSION 5.1.3 Source code file: /home/albert/Downloads/gromacs/gromacs-5.1.3/src/gromacs/gmxlib/gmx_detect_hardware.cpp, line: 458 Fatal error: Incorrect launch

Re: [gmx-users] MPI GPU job failed

Hi, I used your suggested command line, but it failed with the following messages: --- Program gmx mdrun, VERSION 5.1.3 Source code file: /home/albert/Downloads/gromacs/gromacs-5.1.3/src/gromacs/gmxlib/gmx_detect_hardware.cpp, line: 458

Re: [gmx-users] MPI GPU job failed

Hello: I try to run command: gmx_mpi mdrun -nt 2 -v -s 62.tpr -gpu_id 01 but it failed with messages: --- Program gmx mdrun, VERSION 5.1.3 Source code file: /home/albert/Downloads/gromacs/gromacs-5.1.3/src/programs/mdrun/resource

Re: [gmx-users] MPI GPU job failed

Does anybody have any idea? On 08/10/2016 04:03 PM, Albert wrote: Hello: I am trying to submit gromacs jobs with command line: mpirun -np 2 gmx_mpi mdrun -s 61.tpr -v -g 61.log -c 61.gro -x 61.xtc -ntomp 10 -gpu_id 01 However, it failed with messages: Number of GPUs detected: 2

Re: [gmx-users] 5.1.2 doesn't support GTX1080?

Jul 18, 2016 at 4:22 PM Albert <mailmd2...@gmail.com> wrote: Hello: I've installed cuda-8.0 in my Linux OS. Then I compiled Gromacs-5.1.2 with GPU support without any errors. However, when I submit Gromacs job, it always failed with messages: NOTE: Error occurred during GPU

[gmx-users] 5.1.2 doesn't support GTX1080?

36MiB | +-+ Does anybody have any suggestions? Thanks a lot Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] GPU job frequently failed

Hello: I noticed that my GPU job under 5.1.2 often failed with messages: step 52400, will finish Mon Jul 25 12:04:59 2016 --- Program gmx mdrun, VERSION 5.1.2 Source code file: /home/albert/Downloads/gromacs/gromacs-5.1.2/src/gromacs/mdlib

Re: [gmx-users] command line issue

it still doesn't work for CSH On 07/11/2016 05:05 PM, Florent Hédin wrote: Hi, what about using instead the csh file. i.e. source /home/albert/install/gromacs/5.1.2/bin/GMXRC.csh there are several versions of the file, for different shells : -rwxr-xr-x 1 root root 566 Jul 8 11:13

Re: [gmx-users] command line issue

HMMMbut I found that many professional software actually prefer to support CSH.. I am just wondering is it possible to make this useful function also works in csh? thx a lot On 07/11/2016 05:03 PM, Mark Abraham wrote: Hi, Yes, like I said:-) We asked users some years ago, and

Re: [gmx-users] command line issue

Hi: I do add this in my .cshrc: source /home/albert/install/gromacs/5.1.2/bin/GMXRC however, it doesn't work in my tcsh. It seems to work only in Bash. regards On 07/11/2016 04:48 PM, Mark Abraham wrote: Hi, If you have used "source GMXRC" from a supported shell (bash

[gmx-users] command line issue

on correctly? thx a lot Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth

Re: [gmx-users] strange GPU performance

yes. But the job failed from to time: vol 0.87! imb F 34% step 33600, will finish Sat Jul 23 17:26:12 2016 --- Program gmx mdrun, VERSION 5.1.2 Source code file: /home/albert/Downloads/gromacs/gromacs-5.1.2/src/gromacs/mdlib/nbnxn_cuda

[gmx-users] strange GPU performance

is only 4 CPU was using but it generated 16 Gromacs process. The speed of GPU is very slow I am just wondering how to solve this problem? Thanks a lot Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] wrap only in XZ?

.. THX On 06/26/2016 09:06 AM, Tsjerk Wassenaar wrote: Hi Albert, Rotate the system 90 degrees and use PBC in xy only. Cheers, Tsjerk -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * C

[gmx-users] wrap only in XZ?

Hello: I've got a membrane protein system and I would like the water and ions only wrap in XZ direction. Currently, they can also wrap at Z direction. I am just wondering how can we prevent them wrap at Z direction? Thank you very much. Albert -- Gromacs Users mailing list * Please search

Re: [gmx-users] can we analyse Gromacs trajectory with jupyter?

ology" I hope that Dan Roe (cc) can find a time slot to implement xtc and tng parser soon. @Albert: meanwhile, you can absolutely use pytraj (python interface of cpptraj)<https://github.com/Amber-MD/pytraj> and NGLView <https://github.com/arose/nglview> for your

Re: [gmx-users] Gromacs 5.1 build for windows 8. Cygwin compatibility with CUDA/GPU acceleration.

why not install it in Linux instead of wasting time install it in Windows. On 06/24/2016 03:12 PM, timothy.du...@louisville.edu wrote: I have spend the past week trying to figure out how to compile GROMACS for windows. I spend a lot of time on the web and everyone pointed to the use of

[gmx-users] can we analyse Gromacs trajectory with jupyter?

are examples: http://ambermd.org/tutorials/analysis/tutorial_notebooks/nglview_notebook/ http://amber-md.github.io/pytraj/latest/tutorials/plot_correlation_matrix.html I am just wondering can we do similar things in Gromacs? Thx a lot Albert -- Gromacs Users mailing list * Please search

[gmx-users] can we constrain a bond?

Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo

[gmx-users] job failed. Too many CPU?

Hello: I am trying to run a Gromacs job with command line: mpirun -np 1 gmx_mpi grompp -f step6.0_minimization.mdp -o 60.tpr -n -c step5_charmm2gmx.pdb -maxwarn -1 mpirun -np 56 mdrun_mpi -s 60.tpr -g 60.log -c 60.gro >& 60.info I am using Charmm36 FF for my system which contains 60,000

Re: [gmx-users] compile 2016-beta2 failed

HI Mark: But in my machine, all the file from cuda-7.5 development package has been installed. thanks again. On 06/17/2016 10:03 PM, Mark Abraham wrote: Hi, My earlier comments all stand - you need a working cuda compilation environment, and the people to help you do that are the

Re: [gmx-users] compile 2016-beta2 failed

Thanks a lot for such comments. I specified the path of cicc in my .bashrc as the following: export PATH=/opt/common/cuda-7.5/nvvm/bin:$PATH Then compiled it again cmake .. -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs/2016-beta2 -DGMX_GPU=ON -DGMX_MPI=ON -DCUDA_TOOLKIT_ROOT_DIR=/opt

Re: [gmx-users] compile 2016-beta2 failed

HEllo Mark: Thanks a lot for the reply. I replied Gromacs with the following command line: cmake .. -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs/2016-beta2 -DGMX_GPU=ON -DGMX_MPI=ON -DCUDA_TOOLKIT_ROOT_DIR=/opt/common/cuda-7.5 make -j32 But it still failed with messages: Building

[gmx-users] compile 2016-beta2 failed

Hello: I am trying to use the following command line to compile Gromacs-2016 beta2: CMAKE_PREFIX_PATH=/home/albert/install/gromacs/fftw-3.3.4 cmake .. -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs/romacs-2016-beta2 -DGMX_GPU=ON -DGMX_MPI=ON make -j32 but the make step failed

[gmx-users] Fwd: how to convert CHARMM36 system into virtual site system?

Hello: I've built a membrane system from CHARMM-GUI with CHARMM36 FF. I am just wondering how can we convert the lipids molecule to virtual site lipids? Thank you very much Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] how to convert CHARMM36 system into virtual site system?

Hello: I've built a membrane system from CHARMM-GUI with CHARMM36 FF. I am just wondering how can we convert the lipids molecule to virtual site lipids? Thank you very much Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX

[gmx-users] about g_cluster

Hello: I've got a question on g_cluster calculation: shall we superimpose the protein backbone of each frame before we perform g_cluster? Or g_cluster will superimpose automatically before calculation? thx a lot -- Gromacs Users mailing list * Please search the archive at

[gmx-users] why .xtc not generated in 5.1.2?

Hello: I am using the following md.mdp file for MD production in Gromacs-5.1.2: integrator = md dt = 0.002 nsteps = 5000 nstlog = 1 nstxout = 0 nstvout = 0 nstfout = 0

[gmx-users] right hand side error

Hello: I am running command line: gmx_mpi grompp -f step7_production.mdp -c step6.6_equilibration.gro -n index.ndx -p topol.top -o md.tpr in Gromacs-5.1.2. but it always failed with messages: ERROR 1 [file step7_production.mdp, line 42]: Right hand side '5.0 5.0' for parameter 'tau_p'

Re: [gmx-users] GPU efficiency

supports 1GPU+1CPU for a single job. If in the near future, they somehow manage to use multiple GPU for a single job, it will change everything a lot. regards Albert On 01/24/2016 09:54 AM, Mark Abraham wrote: Hi, You need to use the hidden -fasterthanamber mdrun benchmarking option

[gmx-users] GPU efficiency

atic cutoff=10 A: 1x GTX 780 Ti Gromacs-5.0.7: 30 ns/day Amber-14: 44 ns/day Desmond-2015v4: 90 ns/day 2x GTX 780Ti Gromacs-5.0.7: 55 ns/day Amber-14: 75 ns/day Desmond-2015v4: NA (not support multiple GPU running) I am just wondering why? regards Albert -- Gromacs Users mailing list * Pl

[gmx-users] cgenff script failed

Dear: I've trying to use the following command to generate ligand toplogy for Gromacs: cgenff_charmm2gmx.py UNK ligand.mol2 ligand.str ./charmm36.ff but it failed with messages: error in atomgroup.py: read_mol_coor_only: natoms in mol2 .ne. top 54 0 It is really strange to see this error

Re: [gmx-users] cgenff script failed

I see. thx a lot. It works now. ;-) On 01/18/2016 08:33 PM, Justin Lemkul wrote: This probably means your residue isn't named "UNK" in the stream file. -Justin -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] supervised MD in Gromacs?

thors, but it seems that they are reluctant to share any of their methods, protocol or script.. Albert On 12/08/2015 11:26 AM, João Henriques wrote: Dear Albert, You'll have to provide more information. As it is, I doubt anyone understands what you're referring to. What method is it?

Re: [gmx-users] supervised MD in Gromacs?

, they never reply when I request to share their script/configuration file/MD details. regards Albert On 12/08/2015 12:04 PM, João Henriques wrote: _*As far as I know*_, the SuMD algorithm is not implemented in GROMACS. _*I only took a peek at the respective reference*_, but it seems

[gmx-users] supervised MD in Gromacs?

Dear: I noticed that several paper successfully captured the process of ligand binding to a protein deep pocket in tens of ns time scale MD simulations without any biased. It is a really impressive an useful method. I am just wondering can we do this in Gromacs? Thanks a lot Albert

Re: [gmx-users] supervised MD in Gromacs?

, since we can place the ligand with countless pose. In the mentioned "supervised MD", it seems that at least they can reproduce the ligand binding mode observed crystal structure in such a short time.. Do you know any other similar methods can do this? Thanks a lot Albert

Re: [gmx-users] supervised MD in Gromacs?

Thanks for the comments. In this case, it is probably meaningless to compare the kinetic of two ligand based on the time that ligand jump from bulk water into the binding pocket.Neither could one be sure that the final pose is close to the crystal structure. regards Albert On 12

[gmx-users] service broken?

Hello: I am trying to download the latest CHARMM forcefield for Gromacs from: http://mackerell.umaryland.edu/charmm_ff.shtml However, I cannot connect to it in the last 10 days. Does anybody have any idea what's happening? thanks a lot Albert -- Gromacs Users mailing list * Please search

Re: [gmx-users] support mmcif format?

://mmcif.wwpdb.org/docs/faqs/pdbx-mmcif-faq-general.html I wish the developer could pay attention to the evolution of PDBx/mmCIF format. Thank you very much. Albert On 11/23/2015 10:57 AM, Mark Abraham wrote: Hi, We've talked about this internally once or twice, but nobody's taken action. We should probably

Re: [gmx-users] support mmcif format?

: trjconv -f md.xtc -s md.tpr -o test.pdb -sep -b xx -e xx It will lead to many problems from the .PDB file if our system is too big By contrast if it is mmCIF or PDBX format, everything would be perfect. Albert On 11/23/2015 12:08 PM, Hannes Loeffler wrote: It's hard to see for me

[gmx-users] support mmcif format?

of residues, and number of atoms. Thank you very much Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

[gmx-users] g_select problem

Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo

[gmx-users] problem of compiling

Hello: I am trying to compile Gromacs-5.0.7 with command: CC=mpicc CXX=mpicxx F77=mpif90 FC=mpif90 LDF90=mpif90 CMAKE_PREFIX_PATH=/home/albert/install/intel/mkl/include/fftw:/home/albert/install/intel/impi cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=/home

Re: [gmx-users] problem of compiling

I see. How should I turn this option off? thx a lot On 11/03/2015 11:37 AM, Kutzner, Carsten wrote: AVX2 is only supported from gcc 4.7.0 on. Carsten -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

[gmx-users] ligand contact map

Hello: I would like to calculate which residues does my ligand contact with during the MD simulation. I am just wondering is there any module for calculating ligand contact map? Thank you very much Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

[gmx-users] Cl topology in gromacs

Hello: I am using acpype to create ligand topology. However, I noticed that acpype may not recogonize Cl element which is a halogen atom correctly. After acpype, it generate a new ligand pdb file called: lig_NEW.pdb and I found the following: ATOM 10 C09 UNK Z 1 11.502 -10.939

Re: [gmx-users] no GPU detected

Thank you for kind reply. I reinstalled the driver and now Gromacs flies. ragards On 07/08/2015 04:55 PM, Szilárd Páll wrote: Actually, those are errors quite clearly come from_failed_ commands that are aimed at setting up and loading the GPU driver. Nothing to do with GROMACS and no, your

Re: [gmx-users] no GPU detected

Hi Mark: thank you for comments. I am pretty sure that the installation is correct. I found the following for mdrun: Try 'mknod --help' for more information. chown: changing group of '/dev/nvidiactl': Operation not permitted chown: changing group of '/dev/nvidia0': Operation not permitted

[gmx-users] no GPU detected

-smi and can find the GPU without any problem. I've installed CUDA7 in the linux X64 system. thank you very much. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http

[gmx-users] how to configure PBS for GPU workstation for Gromacs?

/torque-5.1.1 --with-nvml-include=/usr/local/cuda/gpukit/usr/include/nvidia/gdk --with-nvml-lib=/usr/local/cuda/lib64 thanks million in advance. Albert -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't

Re: [gmx-users] how can we merge SOL into protein.itp?

I am trying to use GMXPBSAS to calculate the ligand binding energy, but this program will delete all solvent molecules automatically. In this case, I have to merge the protein and crystal water into a single .itp file so that GMXPBSA treat the crystal water as a part of protein However, I

[gmx-users] how can we merge SOL into protein.itp?

that two crystal water molecules was separated from protein.itp, and they only explicitly documented in topol.top file. So I am just wondering how can we solve this problem? thx a lot ALBERT -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support

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