[gmx-users] MD with DNA double strand

Dear Gromacs users, I want to do a molecular dynamic simulation for my enzyme-ligand complex. The enzyme is topoisomerase I. I used the pdb id 1K4T for the simulation and I need to keep the DNA double strand with the enzyme. I replaced the 5'-sulfhydryl group into a 5'-hydroxyl group before start

Re: [gmx-users] on CHARMM-GUI produced lipid bilayer for gromacs use

Hi Brett, The CHARMM-GUI also provides the .top file. You can use that and the PDB (it doesn't need to be .gro) to run grompp. Cheers, Tsjerk On Thu, Sep 17, 2015 at 5:06 AM, Brett wrote: > Dear All, > > > After I got the membrane protein PDB with the membrane part packed in > lipid bilayer b

[gmx-users] g_mmpbsa time

Dear users i simulated a system for 30 nano-seconds(dt=2fs) and my frame was 6 ps for binding free energy computations by g_mmpbsa method in gromacs, my computations took a long time is it correct? can i change my simulation time in *mdp* file for *tpr* production for using in g_mmpbsa calculations

Re: [gmx-users] Atomic charges

Thanks Justin. Things are clearer now. -Pallavi Banerjee -- 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] -rdd and -ddcheck

hi gmx users,i got a problem while running implicit simulation (10 ns) the problem is in bond interactions and it says that i should see option -rdd and -ddcheck. does anyone know how to use these options. thanks in advance. RegardsSana SaeedSoongsil University -- Gromacs Users mailing list * P

[gmx-users] on CHARMM-GUI produced lipid bilayer for gromacs use

Dear All, After I got the membrane protein PDB with the membrane part packed in lipid bilayer by the lipid bilayer builder of CHARMM-GUI, will you please let me know how to get the inputs for the gromacs next step MD process？ For example， if I wand to go directly to the nvt equilibration step

[gmx-users] GPU-accelerated desktop PC for MD simulations

Hi everyone, I want to build a new GPU-accelerated desktop PC for MD simulations of relatively simple protein/carbohydrate systems. No QM-MM simulations is intended for now. For instance, I have been working with a protein of approximately 1500 atoms in the presence of small carbohydrates (<100 at

Re: [gmx-users] Efficiently running multiple simulations

Hi, The log files tell you that you should compile for AVX2_256 SIMD for the Haswell CPUs you have. Do that. Your runs are wasting a fair chunk of the value of the CPU hardware, and your setup absolutely needs to extract every last drop from the CPUs. That means you need to follow the instructions

Re: [gmx-users] Electric double layer, how to add charge

you should edit your topology file (either top or itp) to include explicit charges to each atom. regarding the proper choice of charges, it depends on the surface potential you think your system should have (mind that OPLSAA will typically produce an overestimated potential as compared to experime

[gmx-users] Electric double layer, how to add charge

Hello users, I want to simulate a graphene electric double layer (edl). So far i have used the cnt tutorials and the tutorial for lysozyme in water. All modification to the OPLSAA field parameter (atomname2type.n2t, atomtypes.atp, ffbonded.itp, ffnonbonded.itp) which i have done were with zero

Re: [gmx-users] GMX 5.0.6 on nodes with gpus

On Wednesday, September 16, 2015 03:20:31 PM Mark Abraham wrote: > Hi, > > That's normal - we just didn't write the code to collect and compare the > information. 5.1 is better at this. Anyway, 5.0 mdrun will assume the > second node is the same as the first and proceed. > > Mark > > On Wed, Sep

Re: [gmx-users] Efficiently running multiple simulations

Hi Mark, Here are two links to .log files for running 1 simulation on 1 GPU and 2 CPUs and 8 simulations across all 8 GPUs and 16 CPUs respectively: https://www.dropbox.com/s/ko2l0qlr4kdpt51/md_1GPU.log?dl=0 https://www.dropbox.com/s/chtcv4nqxof64p8/md_8GPUs.log?dl=0 Regards, -Maxwell ___

Re: [gmx-users] Efficiently running multiple simulations

Hi, On Wed, Sep 16, 2015 at 5:46 PM Zimmerman, Maxwell wrote: > Hi Mark, > > Thank you for the feedback. > > To ensure that I am making a proper comparison, I tried running: > mpirun -np 1 mdrun_mpi -ntomp 2 -gpu_id 0 -pin on > and I still see the same pattern; running a single simulation with 1

Re: [gmx-users] g_traj + g_analyze and core dumped error

On 9/16/15 11:48 AM, gozde ergin wrote: Also I did the same calculation for only one atom and did not get any error. Probably because your original command will have 3*9566 floating-point entries per line, which likely can't even be read by GROMACS tools. So analyzing one atom is fine, a

Re: [gmx-users] g_traj + g_analyze and core dumped error

Ok thanks Justin. Than how can I get the time series of total force of the box? g_traj gives the -af all_force.xvg but this is for each atom not a time series means y coordinate is the total force and x coordinate is the atom. On Wed, Sep 16, 2015 at 5:51 PM, Justin Lemkul wrote: > > > On 9/16/

Re: [gmx-users] miscelle formation using ligands only

On 9/16/15 11:01 AM, Chetan Puri wrote: thanks for the suggestion , I used semi-empirical nddo method for charge determination of each molecules and found out that there was huge difference between the charges provided by the prodrug and that calculated by semi-empirical nddo method. So can i m

Re: [gmx-users] g_traj + g_analyze and core dumped error

Also I did the same calculation for only one atom and did not get any error. On Wed, Sep 16, 2015 at 4:39 PM, gozde ergin wrote: > Dear gromacs users; > > I am trying to estimate the force-force auto correlation function. > To do that first I run the command of : > > 'g_traj -f tra.trr -s topo

Re: [gmx-users] Efficiently running multiple simulations

Hi Mark, Thank you for the feedback. To ensure that I am making a proper comparison, I tried running: mpirun -np 1 mdrun_mpi -ntomp 2 -gpu_id 0 -pin on and I still see the same pattern; running a single simulation with 1 GPU and 2 CPUs performs nearly twice as well as running 8 simulations with

Re: [gmx-users] GMX 5.0.6 on nodes with gpus

Hi, That's normal - we just didn't write the code to collect and compare the information. 5.1 is better at this. Anyway, 5.0 mdrun will assume the second node is the same as the first and proceed. Mark On Wed, Sep 16, 2015 at 5:12 PM wrote: > Hello, > > I am running GMX 5.0.6 on 2 nodes of a c

[gmx-users] GMX 5.0.6 on nodes with gpus

Hello, I am running GMX 5.0.6 on 2 nodes of a cluster. Each node has 1 gpu (Tesla k20). In the log file, gmx reports that the program is running on 2 ranks and reports that it detects 1 gpu on one node. However, it says nothing about the gpu on second node. My guess is that this is not normal

Re: [gmx-users] Efficiently running multiple simulations

Hi, On Wed, Sep 16, 2015 at 4:41 PM Zimmerman, Maxwell wrote: > Hi Mark, > > Sorry for the confusion, what I meant to say was that each node on the > cluster has 8 GPUs and 16 CPUs. > OK. Please note that "CPU" is ambiguous, so you should prefer not to use it without clarification. Unless the

Re: [gmx-users] miscelle formation using ligands only

thanks for the suggestion , I used semi-empirical nddo method for charge determination of each molecules and found out that there was huge difference between the charges provided by the prodrug and that calculated by semi-empirical nddo method. So can i modify the charges in the .itp file of variou

Re: [gmx-users] gmx dipoles with dynamic indices (gromacs 5.0.x)

Thank you Justin, Yes, that would do the work. I thought there could be another way, but I won't avoid doing it frame by frame. Thank you again. On Wed, Sep 16, 2015 at 2:55 PM, Justin Lemkul wrote: > > > On 9/15/15 6:13 PM, Daskalakis Vangelis wrote: > >> Hello. >> I want to use a dynamic selec

Re: [gmx-users] Efficiently running multiple simulations

Hi Mark, Sorry for the confusion, what I meant to say was that each node on the cluster has 8 GPUs and 16 CPUs. When I attempt to specify the GPU IDs for running 8 simulations on a node using the "-multi" and "-gpu_id", each .log file has the following: "8 GPUs user-selected for this run. Mapp

[gmx-users] g_traj + g_analyze and core dumped error

Dear gromacs users; I am trying to estimate the force-force auto correlation function. To do that first I run the command of : 'g_traj -f tra.trr -s topol.tpr -of force.xvg' My force.xvg file covers for all atoms in simulation box which I have 9566 atoms. Than I run the command of : 'g_analyze

Re: [gmx-users] Problem with gmx-distance

No, the atoms can be in a single group for this simple case of an atom-atom distance. The next line (after the prompt that you quote) should say something like "(one per line, ..., Ctrl-D to end)". Following those instructions should help (i.e., entering Ctrl-D). Best regards, Teemu On Wed, Sep

Re: [gmx-users] Problem with gmx-distance

On 9/16/15 9:06 AM, Timofey Tyugashev wrote: I want to get the distance between atoms 3770 and 5182 in my trajectory After consulting with the Manual I write command: gmx distance -n ind2.ndx -f trj1_WT_md_40.xtc -s wt_md.gro -oav distav.xvg -oall dist.xvg and index file ind2.ndx: [ LYS_241_ODG

[gmx-users] Problem with gmx-distance

I want to get the distance between atoms 3770 and 5182 in my trajectory After consulting with the Manual I write command: gmx distance -n ind2.ndx -f trj1_WT_md_40.xtc -s wt_md.gro -oav distav.xvg -oall dist.xvg and index file ind2.ndx: [ LYS_241_ODG_C1' ] 3770 5182 The program responds like th

Re: [gmx-users] problem implementing REST2 in GROMACS 4.6.5

Hi, Mark. Thanks a lot for your kind reply. I am filing the issue on the website you mentioned. Please let me know at your earliest convenience whether the problem can be sorted out or it is better to resort to a previous gromacs version in the meanwhile (it seems that REST2 can be implemented easi

Re: [gmx-users] Problem in running CPMD with gmx-3.3.1

Hi, There's nothing here that points to a GROMACS-related issue. I think you should take up the question with the CPMD community. Mark On Wed, Sep 16, 2015 at 1:36 PM Padmani Sandhu wrote: > Hello all, > > *I am running CPMD v4.1 in hybrid with gmx-3.3.1_qmmm-1.3.2. While running > the qmmm_ex

Re: [gmx-users] H-bond calculation

On 9/16/15 4:06 AM, Erik Marklund wrote: Dear RJ, I don’t remember exactly how the groups are treated internally, but I think you might need to include the hydrogen in the donor group. Correct, otherwise there's no way to calculate the H-D-A angle. -Justin --

Re: [gmx-users] gmx dipoles with dynamic indices (gromacs 5.0.x)

On 9/15/15 6:13 PM, Daskalakis Vangelis wrote: Hello. I want to use a dynamic selection scheme (select different atoms based on the same selection criteria for each frame of a trajectory) and pass this selection/ info to the gmx dipoles tool. It seems that the -select option cannot be used. I t

Re: [gmx-users] Fixing periodicity effects on trajectory file

On 9/16/15 1:23 AM, Homa rooz wrote: Dear Justin ​If you asked about verifying docking process​. I should say, I have worked with single chain protein and the best ranked binding energy was -7.41 kcal/mol by AutoDock 4.2, considering that binding site was located on turn structure and the edge

Re: [gmx-users] miscelle formation using ligands only

On 9/15/15 11:01 PM, Chetan Puri wrote: so what is the best option for topologies. A force field you trust in concert with molecules that are individually parametrized using suitable target data. There is a reason why parametrization is considered an expert topic. While there are numer

Re: [gmx-users] Atomic charges

On 9/16/15 12:27 AM, Pallavi Banerjee wrote: Hello users, I have this confusion regarding the atomic charges that gromacs sees. I have defined my residues in aminoacids.rtp file with my own charges, but the atom types for the same in the ffnonbonded.itp have different charges on them. Which of

[gmx-users] Problem in running CPMD with gmx-3.3.1

Hello all, *I am running CPMD v4.1 in hybrid with gmx-3.3.1_qmmm-1.3.2. While running the qmmm_example ethane_em, the mdrun is evoked CPMD but the process was stopped with an error message without completing energy minimization:* MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD wit

Re: [gmx-users] gromacs-5.1 installation error

Hi, https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-July/098940.html Mark On Wed, Sep 16, 2015 at 11:45 AM Brett wrote: > Dear All, > > When I tried to install the gromacs-5.1 by > > "tar xfz gromacs-5.1.tar.gz > cd gromacs-5.1 > mkdir build > cd build > cmake .. -DGMX_BUILD_

[gmx-users] gromacs-5.1 installation error

Dear All, When I tried to install the gromacs-5.1 by "tar xfz gromacs-5.1.tar.gz cd gromacs-5.1 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC". at the "cmake .. -DGMX_BUILD_OWN_FFTW=ON -DRE

Re: [gmx-users] problem implementing REST2 in GROMACS 4.6.5

Hi, That does look like a code problem, but I can't imagine how. Can you please open an issue at http://redmine.gromacs.org, and upload .tpr and .log files so we can see what is going on? Thanks! Mark On Mon, Sep 14, 2015 at 1:22 PM Elio Fiorentini wrote: > I report an example : > > file md0.

Re: [gmx-users] Efficiently running multiple simulations

Hi, I'm confused by your description of the cluster as having 8 GPUs and 16 CPUs. The relevant parameters are the number of GPUs and CPU cores per node. See the examples at http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-features.html#running-multi-simulations Mark On Tue, Sep 15, 2

Re: [gmx-users] Atomic charges

The forcefield is OPLS-AA. I put in the modified charges for the residue in the aminoacids.rtp file. The topology generated also shows the same charges that I put. But I was wondering if the charges defined for the atomtypes in the ffnonbonded.itp overrride these. Thanks and regards, -Pallavi Ban

Re: [gmx-users] H-bond calculation

Dear RJ, I don’t remember exactly how the groups are treated internally, but I think you might need to include the hydrogen in the donor group. Kind regards, Erik > On 16 Sep 2015, at 07:39, RJ wrote: > > Dear gmx, > > > I would like to calculate the H-bond occupancy between two residue (in