Re: [gmx-users] Help installing do_x3dna

Hi Salvador, If you did not have any luck so far, trying to contact the author of the tool, Rajendra Kumar, directly might help: https://scholar.google.com/citations?user=zYKuBCcJ&hl=en Best, Christian On 2019-11-21 21:00, Salvador Herrera-Velarde wrote: Dear All, I am trying to insta

[gmx-users] Help installing do_x3dna

Dear All, I am trying to install do_x3dna in a Linux (Ubuntu Mint) computer where I have already installed gromacs-2019.2. I followed the steps in: https://do-x3dna.readthedocs.io/en/latest/install_do_x3dna.html but without success. I executed the following command: cmake .. -DGMX_PATH=/usr/loca

Re: [gmx-users] Help with a failing test - gromacs 2019.4 - Test 42

Hi Szilard, I just found time to rerun the tests and your suggestion worked. Many thanks for this. Regards, T. On Wed, 16 Oct 2019 at 13:43, Szilárd Páll wrote: > Hi, > > The issue is an internal error triggered by the domain decomposition not > liking 14 cores in your CPU which lead to a pr

Re: [gmx-users] Help with a failing test - gromacs 2019.4 - Test 42

Hi, The issue is an internal error triggered by the domain decomposition not liking 14 cores in your CPU which lead to a prime rank count. To ensure the tests pass I suggest trying to force only one device to be used in make check, e.g. CUDA_VISIBLE_DEVICES=0 make check; alternatively you can run

[gmx-users] Help with a failing test - gromacs 2019.4 - Test 42

Hi, When performing a "make check" on Gromacs 2019.4, I'm getting test 42 failing. It gives the error: Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8 And the mdrun.out and md.log of swap_x reports: The number of ranks you selected (14) contains a

[gmx-users] Help with pull code for umbrella pulling

Hi, I am currently trying to perform an umbrella simulation on a nucleosome structure. I am trying to pull the C-terminal tail away from the rest of the structure. I am at the pulling stage and run: gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -r npt.gro -o pull.

Re: [gmx-users] [HELP] Residue 'NI' not found in residue topology database , Vol 184, Issue 67

On 8/27/19 11:55 AM, Edjan Silva wrote: The only .rtp file is aminoacids.rtp. So should I add NI topological descriptions to this file? Yes. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hal

Re: [gmx-users] [HELP] Residue 'NI' not found in residue topology database , Vol 184, Issue 67

uot;_mm_hadd_pd" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(178): error: > identifier "_mm_cvtsd_f64" is undefined > > /usr/include/c++/4.8.5/x86_64-redhat-linux/bits/opt_random.h(185): error: > identifier "_mm_mul_pd" is

Re: [gmx-users] [HELP] Residue 'NI' not found in residue topology database

On 8/26/19 12:04 PM, Edjan Silva wrote: Dear users, I am trying to perform a simulation with a protein which contains two nickel atoms in the active site. When using the pdb2gmx command the following error appears: 'NI' not found in residue topology database I have edited the ions.itp file

[gmx-users] [HELP] Residue 'NI' not found in residue topology database

Dear users, I am trying to perform a simulation with a protein which contains two nickel atoms in the active site. When using the pdb2gmx command the following error appears: 'NI' not found in residue topology database I have edited the ions.itp file in the force field directory used (opls) but

Re: [gmx-users] Help with generating Arginine topology for Amber FF (Pandya, Akash)

On 7/2/19 12:01 PM, Pandya, Akash wrote: Do I still need to do this if I just want charged arginine (CARG)? Its my understanding that there are three types of arginine residues; ARG, CARG and NARG available. I thought the amino acids are available in gromacs? Sorry if it's a silly question

Re: [gmx-users] Help with generating Arginine topology for Amber FF (Pandya, Akash)

FF in gromacs before. Akash -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se On Behalf Of ABEL Stephane Sent: 02 July 2019 16:18 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Help with generating Arginine topology for Amber FF (Pandya,

[gmx-users] Help with generating Arginine topology for Amber FF (Pandya, Akash)

Hello there are not parameters and RESP charges for standalone residue such as Arg in GROMACS. So you will have to construct a rtp file for this residue and derive the corresponding RESP charges yourself. You could also do a quick in literature to see if some have already done the job for you.

[gmx-users] Help with generating Arginine topology for Amber FF

Hi all, I'm trying to generate topology for arginine. I use the following command: gmx pdb2gmx -f Arginine.pdb -o Arg.gro -inter -water tip3p I get the following error: Fatal error: In the chosen force field there is no residue type for 'ARG' as a standalone (starting & ending) residue Please

Re: [gmx-users] HELP - Fatal error gmx pdb2gmx

On 5/13/19 9:33 AM, Edjan Silva wrote: HELP - Fatal error gmx pdb2gmx (Justin Lemkul) Yes. Includes residues in residuetypes.dat. however the same error remains. I can't see how that happens. Please post the full screen output of pdb2gmx from the failed command (and please don't reply to t

Re: [gmx-users] help OpenCL build failure

Hi, I’ve pasted below an email that I sent to this list a few months ago after receiving some help building GROMACS on my MacBook with AMD GPU. This was with a slightly earlier version of GROMACS but it may still be helpful. Mike ——— Hi again Szilárd, I just wanted to follow up on my last m

Re: [gmx-users] help OpenCL build failure

Hi, Have you tried to use the cmake curse interface: ccmake .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DGMX_GPU=ON -DGMX_USE_OPENCL=ON What version of OS X are you using? Manual indicates may need 10.10.4 or higher if using an AMD GPU (http://manual.gromacs.

[gmx-users] help OpenCL build failure

Hi I have successfully installed Gromacs version 2018.6 (non-GPU version: with the following values: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DBUILD_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX='usr/local/gromacs/2018.6/' I am not able to generate makefile for t

Re: [gmx-users] HELP - Fatal error gmx pdb2gmx

On 5/10/19 2:26 PM, Edjan Silva wrote: I deleted all non-protein molecules and saved the file. I typed the following command: *gmx pdb2gmx -f 4gy7.pdb -o conf.gro -ignh* The error was as follows: *Fatal error:* *The residues in the chain MET1--PHE840 do not have a consistent type. The* *fir

[gmx-users] HELP - Fatal error gmx pdb2gmx

I deleted all non-protein molecules and saved the file. I typed the following command: *gmx pdb2gmx -f 4gy7.pdb -o conf.gro -ignh* The error was as follows: *Fatal error:* *The residues in the chain MET1--PHE840 do not have a consistent type. The* *first residue has type 'Protein', while residue

Re: [gmx-users] Help for GROMACS best performance system

Hi, The recent paper https://arxiv.org/abs/1903.05918 is excellent for these questions, and more! Mark On Sat., 20 Apr. 2019, 21:09 Ali Sufali, wrote: > Hi > > It's been a while I have started using GROMACS for my researches and now I > want to buy a system with powerful performance. > > I wan

Re: [gmx-users] Help for GROMACS best performance system

Hi, The answer to this question is very system dependent, so my suggestion is to run a benchmark simulation. If you're simulating a system in explicit solvent, the performance will remain pretty much stable in time, so you can run a very short simulation (i.e. 100ps) and check at the end of the log

[gmx-users] Help for GROMACS best performance system

Hi It's been a while I have started using GROMACS for my researches and now I want to buy a system with powerful performance. I want to choose between these two options Is it better to have multiple graphics card on a 12-24 core system or it is better to have one or two graphics card on multiple

[gmx-users] Help needed in using gmx select

Dear Gromacs Developers and Users, I need a small help in GROMACS trajectory analysis. I want to define a selection i.e., 4Ang volume around two residues (from different chains X and chain Y ) that make your binding site --- Within this selection I want count number of waters molecules along th

[gmx-users] Help needed using gmx select of GROMACS

Dear Gromacs Developers and Users, I need a small help in GROMACS trajectory analysis. I want to define a selection i.e., 4Ang volume around two residues (from different chains X and chain Y ) that make your binding site --- Within this selection I want count number of waters molecules along th

[gmx-users] Help regarding clustering of conformations

hello, i have the output files of 100ns production simulations. I have treated for PBC. I want to find clusters of the trajectories. This can be done using gmx cluster. But i want to do energy minimization of each snapshot in the trajectory and then make clusters. Is there any command or option or

Re: [gmx-users] Help regarding clustering of conformations

hello, i have the output files of 100ns production simulations. I have treated for PBC. I want to find clusters of the trajectories. This can be done using gmx cluster. But i want to do energy minimization of each snapshot in the trajectory and then make clusters. Is there any command or option or

Re: [gmx-users] help for debye waller factor calcuations

ETH Zurich From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of wangshaof...@iae.ac.cn [wangshaof...@iae.ac.cn] Sent: Monday, February 11, 2019 8:06 AM To: gromacs.org_gmx-users Subject: [gmx-users] help

[gmx-users] help for debye waller factor calcuations

Dear all, I am trying to calculate mean square relative displacement (MSRD), debye-waller factor, of single or multiple scattering of EXAFS spectra. Can any expert introduce how to calculate them using gromacs tools or some other tools? Any help is appreciated. Best, Shaofeng Wang Ph.D Emai

Re: [gmx-users] Help for using Lincs along with constraint

On 2/3/19 10:00 AM, anupama sharma wrote: Dear user's I need help for using lincs along with constraint. I am doing water (tip4p/2005) and carbon nanotube simulation and since I am using tip4p/2005, I had used exclusion for rigid body dynamics and for that I kept lincs off. But after nvt si

Re: [gmx-users] Help regarding applying constraint on individual molecule in a system

On 2/1/19 10:24 AM, anupama sharma wrote: Dear user's, I need help regarding constraint. I am doing simulation of water ( tip4p/2005) and carbon nanotube and want to put constraint only on carbon nanotube as after nvt simulation I had observed that carbon nanotube is getting deformed. W

[gmx-users] Help for using Lincs along with constraint

Dear user's I need help for using lincs along with constraint. I am doing water (tip4p/2005) and carbon nanotube simulation and since I am using tip4p/2005, I had used exclusion for rigid body dynamics and for that I kept lincs off. But after nvt simulation bonds in carbon nanotube is getting bro

[gmx-users] Help regarding applying constraint on individual molecule in a system

Dear user's, I need help regarding constraint. I am doing simulation of water ( tip4p/2005) and carbon nanotube and want to put constraint only on carbon nanotube as after nvt simulation I had observed that carbon nanotube is getting deformed. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Help with respect to processing protein with FE2+

Dear Justin, I had installed ambertools and followed the tutorial - http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm Currently, I am using gaussian to run the optimization part for obtaining parameters. During the process, I realized that the ligand is not picked up as a residue interac

Re: [gmx-users] Help w.r.t enhancing the node performance for simulation

Dear all, Could you please tell me, if this is normal during running a simulation. I am running mdrun with -v flag and i receive this, . . vol 0.23! imb F 2264% pme/F 0.57 step 1496300, will finish Mon Jan 21 00:13:42 2019 vol 0.23 imb F 3249% pme/F 0.75 step 1496400, will finish Mon Jan 21 00:13

[gmx-users] Help with gmx select

Hello, I want to use gmx select to get a list of protein residues that interact with PO4 beads (CG) in a bilayer: The command I am using is: gmx select -s system.gro -f traj.xtc -oi contacting_residues_DOPG.dat -resnr number -n PO4_index_1.ndx -select 'group Protein and same residue as withi

Re: [gmx-users] Help w.r.t enhancing the node performance for simulation

Dear all, I was able to overcome the issue, by introducing the command "mpirun -np x" before the command. Here is the exact command- mpirun -np 32 gmx_mpi mdrun -v -deffnm md_0_10 -cpi md_0_10.cpt -append -ntomp 4 Thank you. On Fri, Dec 28, 2018 at 12:12 PM Prasanth G, Research Scholar < prasan

[gmx-users] Help w.r.t enhancing the node performance for simulation

Dear all, Though the GROMACS was configured with MPI support during installation. installation cmake.txt I am able to use only one MPI process on the node for the simulation. This happens when

Re: [gmx-users] Help with respect to processing protein with FE2+

On 12/24/18 10:11 AM, Prasanth G, Research Scholar wrote: Dear all, One of the proteins of my interest, has a FE2+ in the center and as it plays a main role in the activity of the protein, it cannot be removed. Can you please suggest a solution. I have tried with CHARMM and GROMOS, with no su

[gmx-users] Help with respect to processing protein with FE2+

Dear all, One of the proteins of my interest, has a FE2+ in the center and as it plays a main role in the activity of the protein, it cannot be removed. Can you please suggest a solution. I have tried with CHARMM and GROMOS, with no success. After reading a bit, I understood that, the charges on

Re: [gmx-users] HELP

Hi, Please try to use a descriptive subject for your email... you'll have a better chance of getting the help you actually want ;-) On Tue, Nov 20, 2018 at 3:40 PM Emmanuel Broni wrote: > Hello Gromax Users, > I was running a 100ns MD simulation on an hpc and it was terminated with > the follow

[gmx-users] HELP

Hello Gromax Users, I was running a 100ns MD simulation on an hpc and it was terminated with the following comments in the log file. What does it mean and what do I do? DD step 39 load imb.: force 17.8% pme mesh/force 0.925 step 120 Turning on dynamic load balancing, because the performance lo

Re: [gmx-users] Help

Hi, I could see that you are installing GROMACS 2018. There is the more recent patch release called GROMACS 2018.2, which you should prefer because it fixes some issues while doing the same job as 2018. Mark On Wed, Jul 11, 2018 at 2:13 PM Maximiliano Sebastián Castillo < mcasti...@itba.edu.ar>

Re: [gmx-users] Help

https://www.urbandictionary.com/define.php?term=btw :) He wants you to try never version 2018.2: ftp://ftp.gromacs.org/pub/gromacs/gromacs-2018.2.tar.gz Also try different fftw options. On cmake line add: -DGMX_FFT_LIBRARY=xxx where xxx can be fftw, mkl or fftpack. You also need proper stuff inst

Re: [gmx-users] Help

Sorry, but... what is BTW 2018.2? Another software? El mié., 11 jul. 2018 a las 6:50, Mark Abraham () escribió: > Hi, > > I haven't seen that, and don't know how to guess what might make it work. > BTW 2018.2 is a better idea to install. > > Mark > > On Wed, Jul 11, 2018 at 3:34 AM Maximiliano Se

Re: [gmx-users] Help

Hi, I haven't seen that, and don't know how to guess what might make it work. BTW 2018.2 is a better idea to install. Mark On Wed, Jul 11, 2018 at 3:34 AM Maximiliano Sebastián Castillo < mcasti...@itba.edu.ar> wrote: > Hello, > I have the next problem: > [ 1%] No patch step for 'fftwBuild' >

[gmx-users] Help

Hello, I have the next problem: [ 1%] No patch step for 'fftwBuild' [ 1%] No update step for 'fftwBuild' [ 1%] Performing configure step for 'fftwBuild' checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... configure: error: unsafe srcdir valu

Re: [gmx-users] help me in understanding PCA

Dear gromacs users, Earlier mail contains spread sheet calculation for first element. But I have mentioned 1row 2column please ignore that. My intension is to understand the meaning of all elements. Thank you With Regards Upendra N Research Scholar Department of Studies in Physics,Manasagangotr

[gmx-users] help me in understanding PCA

Dear gromacs users, I am trying to understand covariance matrix produced in the covariance analysis. For understanding purpose, I have simulated 4 residue peptide (10ps, 6 frames ) and constructed covariance matrix for c-alpha atoms. matrix is in 48x3 form (but it is supposed to be 16x16 as per

[gmx-users] Help simulating flow

Hello gmx_users, I am stuck on my simulation and not sure how to implement things in gromacs. Basically, I am looking to simulate flow of solvent over a lipid bilayer. I have a system (created by Charmm-GUI) of lipids and solvent (two separate group IDs in the gromacs) and I would like to apply

[gmx-users] help with orientation restraints

Hi all;I am an amateur gromacs user, but i have read all the tutorials i could find on how to perform md simulations using gromacs, however i still cant find any tutorial about how to include orientation restraints in my simulations. i want to perform a simulation on a helical protein and includ

Re: [gmx-users] Help with interpreting message for fatal error

Hi Justin, Thanks again for the tip. I'm always assuming that there's something wrong with my setup but I tested using one rank only and then I get an order of magnitude smaller fluctuations... #underInvestigation -- Viveca On Mon, Mar 12, 2018 at 6:42 PM, Justin Lemkul wrote: > > > On 3/12/1

Re: [gmx-users] Help with interpreting message for fatal error

Hi Gregory, It's periodically connected and I am applying adaptive biasing/pulling (forgot to say). If you have special experience with that kind of setup, I'd be interested in hearing it. Otherwise, it's quite standard, and yes, parmbsc1. -- Viveca On Mon, Mar 12, 2018 at 6:53 PM, Gregory Poon

Re: [gmx-users] Help with interpreting message for fatal error

On 3/12/18 1:40 PM, Viveca Lindahl wrote: Hi Justin, I'm using semi-isotropic pressure coupling and the periodicity is along z. I should say that I'm also adaptively biasing a base pair to open, which is triggering the fluctuations. I guess you mean using only OpenMP? I have not tried that no

Re: [gmx-users] Help with interpreting message for fatal error

Hi Justin, I'm using semi-isotropic pressure coupling and the periodicity is along z. I should say that I'm also adaptively biasing a base pair to open, which is triggering the fluctuations. I guess you mean using only OpenMP? I have not tried that no, thanks for the suggestion. Now I changed to

Re: [gmx-users] Help with interpreting message for fatal error

Hi Viveca, Could you share more details of your simulations that may shed any light?  I assume that you are using parmbsc1 as the DNA forcefield.  Is it an "unusual" system?  We (and I am sure others) simulate DNA (± ligand) quite a bit and would be as interested in understanding what is goin

Re: [gmx-users] Help with interpreting message for fatal error

On 3/12/18 10:42 AM, Viveca Lindahl wrote: Hi Gregory, In the sense that I see it happening repeatedly yes :) But I can't reproduce it very predictably. After seeing that (for my small system) I get very large box vector fluctuations using Parrinello-Rahman, my current assumption is that ther

Re: [gmx-users] Help with interpreting message for fatal error

Hi Gregory, In the sense that I see it happening repeatedly yes :) But I can't reproduce it very predictably. After seeing that (for my small system) I get very large box vector fluctuations using Parrinello-Rahman, my current assumption is that there are some stability assumptions made by mdrun

Re: [gmx-users] Help with interpreting message for fatal error

Since there hasn't been any response to your question yet, may I ask: is it reproducible? Gregory On 3/11/2018 7:30 AM, Viveca Lindahl wrote: Hi, I'm running a simulation of a periodic DNA molecule. After some time I get, sometimes the following error message: --- A list of mis

[gmx-users] Help with interpreting message for fatal error

Hi, I'm running a simulation of a periodic DNA molecule. After some time I get, sometimes the following error message: --- A list of missing interactions: Proper Dih. of 3917 missing 1 Molecule type 'DNA_chain_A' the first 10 missing interactions, except for exclusio

[gmx-users] Help in stretching membrane

Dear gromacs users, I am totally new to membrane simulation. I wish to simulate a membrane-protein system with applied pressure (say -100 bar). I have read from the user forums and gromacs manual that I can achieve this either by semiisotropic coupling where I can explicitly give the pressure on

Re: [gmx-users] help with my errors (RAHUL SURESH)

On 1/19/18 7:09 AM, RAHUL SURESH wrote: On Fri, Jan 19, 2018 at 4:59 PM, banijamali_fs wrote: Hi there, 1. I'm working on MOF (metal organic framewoks) structures. I'd like to know that if in our topology file we get a decimal figure for the qtot, in which step we made a mistake? and how we

Re: [gmx-users] help with my errors (RAHUL SURESH)

On Fri, Jan 19, 2018 at 4:59 PM, banijamali_fs wrote: > > Hi there, > > > > 1. I'm working on MOF (metal organic framewoks) structures. I'd like to > > know that if in our topology file we get a decimal figure for the qtot, > > in which step we made a mistake? and how we can rectify this? > qtot

Re: [gmx-users] help with my errors (RAHUL SURESH)

> Hi there, > > 1. I'm working on MOF (metal organic framewoks) structures. I'd like to > know that if in our topology file we get a decimal figure for the qtot, > in which step we made a mistake? and how we can rectify this? > > 2. Another question that I have is that when I want to run this

Re: [gmx-users] help with my errors

On Fri, Jan 19, 2018 at 2:12 PM, banijamali_fs wrote: > Hi there, > > 1. I'm working on MOF (metal organic framewoks) structures. I'd like to > know that if in our topology file we get a decimal figure for the qtot, > in which step we made a mistake? and how we can rectify this? > > 2. Another q

[gmx-users] help with my errors

Hi there, 1. I'm working on MOF (metal organic framewoks) structures. I'd like to know that if in our topology file we get a decimal figure for the qtot, in which step we made a mistake? and how we can rectify this? 2. Another question that I have is that when I want to run this command, gmx g

Re: [gmx-users] Help to interpret the energy terms for gmx energy

Hi, On Wed, Dec 6, 2017, 3:11 AM Jose wrote: > Hi all, > > My simulated system is a lipid bilayer of lipid+cholesterol simulated > with coulombtype=PME. I have calculated the energy terms corresponding > to Coul-SR and LJ-SR as a measure of the electrostatic and van der Waals > interactions. How

[gmx-users] Help to interpret the energy terms for gmx energy

Hi all, My simulated system is a lipid bilayer of lipid+cholesterol simulated with coulombtype=PME. I have calculated the energy terms corresponding to Coul-SR and LJ-SR as a measure of the electrostatic and van der Waals interactions. However after reading some literature and posts I have a

[gmx-users] help with wham analysis

Dear Gromacs users, I used gmx wham to obtain the "profile.xvg" with PMF. However, I see that all the values in the second column (Energy) in the profile.xvg are zeroes. Can someone please explain what could cause this? I am using the below lines for the pull code inside the mdp file for the

[gmx-users] Help with segmentation fault error

Hi, I have installed 5.1.1, and am trying to run the simulations. During the run, I am getting this error as pasted below: WARNING: Listed nonbonded interaction between particles 1 and 9 at distance 9.500 which is larger than the table limit 2.030 nm. This is likely either a 1,4 interaction, or a

Re: [gmx-users] Help on MD performance, GPU has less load than CPU.

So the state of the art in the whole field is to just blindly copy .mdp settings from webpages rather than review the literature of related work? Nice. :-D Mark On Thu, Jul 13, 2017 at 7:18 PM Téletchéa Stéphane < stephane.teletc...@univ-nantes.fr> wrote: > Le 12/07/2017 à 18:15, Mark Abraham a

Re: [gmx-users] Help on MD performance, GPU has less load than CPU.

Le 12/07/2017 à 18:15, Mark Abraham a écrit : Hi, Sure. But who has data that shows that e.g. a free-energy calculation with the defaults produces lower quality observables than you get with the defaults? Mark Hi, As defaults are defaults ... who knows :-) To get number in front of these as

Re: [gmx-users] Help on MD performance, GPU has less load than CPU.

Hi, Sure. But who has data that shows that e.g. a free-energy calculation with the defaults produces lower quality observables than you get with the defaults? Mark On Wed, Jul 12, 2017 at 5:59 PM Téletchéa Stéphane < stephane.teletc...@univ-nantes.fr> wrote: > Le 11/07/2017 à 15:24, Mark Abraha

Re: [gmx-users] Help on MD performance, GPU has less load than CPU.

Le 11/07/2017 à 15:24, Mark Abraham a écrit : Guessing wildly, the cost of your simulation is probably at least double what the defaults would give, and for that cost, I'd want to know why. Estimated colleague, Since this is a wild guess, I'd think to add some guesses myself. I remember "some

Re: [gmx-users] Help on MD performance, GPU has less load than CPU.

Hi, I'm genuinely curious about why people set ewald_rtol smaller (which is unlikely to be useful, because the accumulation of forces in single precision will have round-off error that means the approximation to the correct sum is not reliably accurate to more than about 1 in 1e-5), and thus pme_o

[gmx-users] Help on MD performance, GPU has less load than CPU.

Hi, I am working on a node with Intel(R) Xeon(R) CPU E5-2630 v3 @ 2.40GHz, 16 physical core, 32 logical core and 1 GPU NVIDIA GeForce GTX 980 Ti. I am launching a series of 2 ns molecolar dynamics simulations of a system of 6 atoms. I tried diverse setting combination, but however i obtained t

[gmx-users] Help: Illegal divion by zero lipid+protein+solvent

Hello gromacs users: I know this question is very common but i have this problem: I´m trying to obtain area per headgropu of a dppc+protein+solvent membrane and when i use GRIDMaAT it appears: illegal division by zero. My coord_file is my gro file, file type is gro, num_frames 1, num lipid t

Re: [gmx-users] Help in a thermalization

It worked. Thanks Justin. 2017-03-27 18:23 GMT-03:00 Justin Lemkul : > > > On 3/27/17 5:17 PM, Graziele Bortolini wrote: > >> The error 3 was solved, but when I change to cutoff-scheme = group, I >> receive: >> >> "Fatal error: >> The largest charge group contains 66 atoms. The maximum is 32." >>

Re: [gmx-users] Help in a thermalization

On 3/27/17 5:17 PM, Graziele Bortolini wrote: The error 3 was solved, but when I change to cutoff-scheme = group, I receive: "Fatal error: The largest charge group contains 66 atoms. The maximum is 32." I've tried to make this before, and I saw your answer about this error in this link: https

Re: [gmx-users] Help in a thermalization

The error 3 was solved, but when I change to cutoff-scheme = group, I receive: "Fatal error: The largest charge group contains 66 atoms. The maximum is 32." I've tried to make this before, and I saw your answer about this error in this link: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-

Re: [gmx-users] Help in a thermalization

On 3/27/17 4:50 PM, Graziele Bortolini wrote: I do it too, my .mdp file now is like : - cpp = /lib/cpp integrator = md dt = 0.001 nsteps = 50 nstcomm = 1 comm-mode = angular nstxout = 0 nstvout = 0 nstlog = 0 nstenergy = 50 nstxtcout = 50 energygrps = PSB nstlist = 10 ns_type = grid rli

Re: [gmx-users] Help in a thermalization

I do it too, my .mdp file now is like : - cpp = /lib/cpp integrator = md dt = 0.001 nsteps = 50 nstcomm = 1 comm-mode = angular nstxout = 0 nstvout = 0 nstlog = 0 nstenergy = 50 nstxtcout = 50 energygrps = PSB nstlist = 10 ns_type = grid rlist = 0 coulombtype = Cut-off optimize_fft = yes rc

Re: [gmx-users] Help in a thermalization

On 3/27/17 4:12 PM, Graziele Bortolini wrote: When I tried to do a thermalization for a PSB molecule (it has 66 atoms), in vacuum, the molecule rotate around the center of mass. This's my .mdp file: --- cpp = /lib/cpp integrator = md dt = 0.001 nsteps = 50 nstcomm = 1 nstxou

[gmx-users] Help in a thermalization

When I tried to do a thermalization for a PSB molecule (it has 66 atoms), in vacuum, the molecule rotate around the center of mass. This's my .mdp file: --- cpp = /lib/cpp integrator = md dt = 0.001 nsteps = 50 nstcomm = 1 nstxout = 0 nstvout = 0 nstlog = 0 nstenergy = 50 nstxtc

[gmx-users] help me

In simulation  using  following command grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr i need to convert dppc128.pdb to dppc128.gro using this command pdb2gmx -f dppc128.pdb -o dppc128.gro -ignh -ter -water spc but now i am getting this fatal error. Fatal error:There were46 mi

[gmx-users] help to install gromacs in a windows system

Hi, I need seriously help to install gromacs in a system windows 7-64bits. All the videos I found on YouTube are talking about Linux system ignoring Windows. I could just install a Borland C/C++ compiler. For the cmake and gromacs it self I have all the problems. Please to help me (A YouTube lin

[gmx-users] help

Dear all, I want to calculate the diffusion coefficient of a single coarse-grained polymer adsorbed on a wall with Gromacs 5.0.7, where the wall's type is 9-3 and the density is set as 1. Firstly, I use the "gmx msd" command to calculate the diffusion coefficient. The calculation error

Re: [gmx-users] Help with MD of water

Hi, There is a method in gromacs to insert water molecules into a box of size defined by you. Depending on the version of gromacs you have, it will be something like gmx insert-molecules. Dan On Tuesday, August 9, 2016, Omamuyovwi Akemu wrote: > Dear Gromacs Users, > I will like to do a molecu

Re: [gmx-users] Help with gmx make_ndx

It is difficult to understand what is the problem from your mail. if you are unable to use make_ndx try as follows Copy the atoms you wanted to make as one group manually create a group name and paste it. You have to take care the mdp options such as energy groups and t-coupling -- Gromacs Users

Re: [gmx-users] Help with gmx make_ndx

Mark Abraham: > If you want to engage in discussion, please don't subscribe to the digest > and then reply to its emails. That makes it painful for everyone to follow > the discussion. I'm very sorry for my stupid ( I am new to mailing list so not familiar with reply) >> I think if I type 8|9 then

Re: [gmx-users] Help with gmx make_ndx

Hi, If you want to engage in discussion, please don't subscribe to the digest and then reply to its emails. That makes it painful for everyone to follow the discussion. Quyen said: > thanks for your replying, > I think if I type 8|9 then my index.ndx should not appear [systems] group ( > it too l

Re: [gmx-users] Help with gmx make_ndx

Hi, What do you think is wrong about the contents of the index group that was made? Mark On Tue, Aug 23, 2016 at 6:26 PM Quyen V. Vu wrote: > Dear gromacs user, > my system contain such groups: > > 0 System : 943920 atoms > 1 DNA : 3198 atoms > 2 LA

[gmx-users] Help with gmx make_ndx

Dear gromacs user, my system contain such groups: 0 System : 943920 atoms 1 DNA : 3198 atoms 2 LA :76 atoms 3 CL : 130 atoms 4 Water : 940516 atoms 5 SOL : 940516 atoms 6 non-Water

Re: [gmx-users] Help with MD of water

Hey, there are tutorials from Justin Lemkul which should fit your demands and guide you through: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/ Best, Jan Am 09.08.16 um 20:03 schrieb Omamuyovwi Akemu: Dear Gromacs Users, I will like to do a molecular dynamics simul

[gmx-users] Help with MD of water

Dear Gromacs Users, I will like to do a molecular dynamics simulation of water in gromacs. Thereafter obtain thermodynamics observable like potential energy and well as structural and dynamics properties of the system. However, I kindly request for help with the topology file (.top) and molecula

Re: [gmx-users] Help with installation of gromacs

use source /usr/local/gromacs/bin/GMXRC before executing pdb2gmx On Thu, Jul 21, 2016 at 12:36 PM, Sidra Rafi wrote: > Dear Omamuyovwi, > > You have to define your path variable. you can use bash for this purpose. > then it will work. > > > > On Wed, Jul 20, 2016 at 8:49 PM, Omamuyovwi Akemu <

Re: [gmx-users] Help with installation of gromacs

Dear Omamuyovwi, You have to define your path variable. you can use bash for this purpose. then it will work. On Wed, Jul 20, 2016 at 8:49 PM, Omamuyovwi Akemu wrote: > Dear Gromacs User, My name is Jolayemi Omamuyovwi. I am trying to install > gromacs on computer. I went through the instruc

[gmx-users] Help with installation of gromacs

Dear Gromacs User,  My name is Jolayemi Omamuyovwi. I am trying to install gromacs on computer. I went through the instruction in the INSTALL file in gromacs-5.1.2. It looked right but when I do pdb2gmx on the terminal in the directory of my build folder just to know if if gromacs has been prope

Re: [gmx-users] help required in calculation of domain decomposition for a mixed lipid vesicle system

On 5/24/16 6:35 AM, Antara mazumdar wrote: Dear gromacs users, I am trying to calculate domain decomposition of a mixed lipid vesicle system OF SIZE 268675 Atoms and box size is 32 X 32 X 32 nm to be able to run in parallel. I want to calculate the number of PME nodes per total number of nod

[gmx-users] help required in calculation of domain decomposition for a mixed lipid vesicle system

Dear gromacs users, I am trying to calculate domain decomposition of a mixed lipid vesicle system OF SIZE 268675 Atoms and box size is 32 X 32 X 32 nm to be able to run in parallel. I want to calculate the number of PME nodes per total number of nodes. However, i am not clear on how to calculate

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