Re: [gmx-users] Simulation of nonaqueous solvents

Hi, On Mon, Jan 4, 2016 at 6:57 PM abhishek khetan wrote: > Is there a procedure/tutorial/method to calculate ssimulate ions in > non-aqueous solvents from scratch? The general advice is here http://www.gromacs.org/Documentation/How-tos/Parameterization, but for relatively

Re: [gmx-users] Simulation of nonaqueous solvents

On 04/01/16 18:56, abhishek khetan wrote: Is there a procedure/tutorial/method to calculate ssimulate ions in non-aqueous solvents from scratch? By "scratch" I mean that the the solvents I am trying to use (like dimethylsulfoxide or tetrahydrofuran or acetonitrile) and the ions ( Li+, Na+, etc

Re: [gmx-users] Problem in Free Energy Calculations

Hii Justin, Thanks for the suggestion. When I am performing the ligand simulation in water I am getting the following error in nvt equilibration: Program mdrun, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/mdlib/domdec_top.c, line: 393 Fatal error: 56 of the 13118 bonded

Re: [gmx-users] Problem using gromacs

Since you have added the co-ordinayes of jz4 into the CONF.GRO. Therefore to reflect this change you have to increment the second line of conf.gro so that it shows total atoms of the system means protein+ ligand. On Mon, Jan 4, 2016 at 2:57 PM, soumi wrote: > Respected

Re: [gmx-users] Problem in Free Energy Calculations

On 1/4/16 6:25 AM, shagun krishna wrote: Hii Justin, Thanks for the suggestion. When I am performing the ligand simulation in water I am getting the following error in nvt equilibration: Program mdrun, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/mdlib/domdec_top.c, line:

Re: [gmx-users] Problem using gromacs

On 1/4/16 4:27 AM, soumi wrote: Respected Sir, I am new user of gromacs. When I use the following command gmx grompp -f ions.mdp -c 1aki_solv.gro -p topol.top -o ions.tpr I get the following error :Number of coordinates in coordinate file does not match topology file. Please

Re: [gmx-users] Force-switch algorithm

Thank you for your reply, Mark! I have now thought of modifying my input potential, that is, making changes to the tabulated form of potential. I don't really understand the difference between the algorithms of force-switch and potential-switch. Does force-switch algorithm directly act on the

[gmx-users] Problem using gromacs

Respected Sir, I am new user of gromacs. When I use the following command gmx grompp -f ions.mdp -c 1aki_solv.gro -p topol.top -o ions.tpr I get the following error :Number of coordinates in coordinate file does not match topology file. Please tell me how can I correct the number

[gmx-users] Restarting Simulations

Dear Gromacs Users, I am trying to restart a simulation using the following command gmx convert-tpr -s topol.tpr -nsteps 1 -o topol2.tpr mdrun_mpi -s topol2.tpr -cpi state.cpt >& mdrun2_output.log But it doesn't run even a single step. The last few lines read: "starting mdrun 'Protein

Re: [gmx-users] Restarting Simulations

On 1/4/16 6:55 PM, Soumya Lipsa Rath wrote: Dear Gromacs Users, I am trying to restart a simulation using the following command gmx convert-tpr -s topol.tpr -nsteps 1 -o topol2.tpr mdrun_mpi -s topol2.tpr -cpi state.cpt >& mdrun2_output.log But it doesn't run even a single step.

Re: [gmx-users] fix simulation box corners NVE

Hi, I suspect the question is ill-formed. In what way are the corners not fixed when you run NVE/T? All you need to do is turn off pressure coupling. Kind regards, Erik > On 4 Jan 2016, at 21:42, Sereda, Yuriy Vladimirovich > wrote: > > How to fix corners of the NVE or

Re: [gmx-users] fix simulation box corners NVE

Thanks, this helps a bit, now I can be more specific: does particle ever cross the boundary of the box as given by the lattice vectors (last row in *.gro frames ?) 0..Lx, 0..Ly, 0..Lz during NVT or NVE? E.g., can x, y, or z become <0 ? Yuri От:

[gmx-users] Scripts to the gromacs

Hey all, I wish I can find a way to help me writing a script to the gromacs. I mean by scripts "the commands that one writes to gramacs terminals and the choices, which are prompted after command's processing, all collected in one file" I do simulation like lysozyme in water tutorial. Looking

Re: [gmx-users] Force-switch algorithm

Hi Mark, Thank you for your reply. I want to implement this wacky idea because a part of the potential of the system needs to be input in a tabulated form (referring to Iterative Boltzmann Inversion) and the other part (solvent-solvent) interaction is defined by sigma and epsilon, which I again

Re: [gmx-users] Force-switch algorithm

On 1/4/16 10:41 PM, Pallavi Banerjee wrote: Hi Mark, Thank you for your reply. I want to implement this wacky idea because a part of the potential of the system needs to be input in a tabulated form (referring to Iterative Boltzmann Inversion) and the other part (solvent-solvent) interaction

Re: [gmx-users] Problem using gromacs

in OPLS ff when i use tip3p water i got this error but if tip3p selected then there no problem and it's interesting! On Mon, Jan 4, 2016 at 2:18 PM, Justin Lemkul wrote: > > > On 1/4/16 4:27 AM, soumi wrote: > >> Respected Sir, >>I am new user of gromacs.

Re: [gmx-users] FFTW with AVX

Ah great, sorry. Google showed me the old version (for the 5.0 release) of the site! Great work, thanks! On 01/04/2016 03:02 PM, Mark Abraham wrote: Hi, No, http://manual.gromacs.org/documentation/5.1.1/install-guide/index.html#using-fftw is consistent - use both --enable-sse2 and

Re: [gmx-users] FFTW with AVX

Hi, No, http://manual.gromacs.org/documentation/5.1.1/install-guide/index.html#using-fftw is consistent - use both --enable-sse2 and --enable-avx. Earlier documentation was incomplete - the important thing is that even if the hardware is AVX, with up to and including FFTW 3.3.4, performance is

Re: [gmx-users] Problem using gromacs

On 1/4/16 8:20 AM, masoud keramati wrote: in OPLS ff when i use tip3p water i got this error but if tip3p selected then there no problem and it's interesting! This comment makes no sense. Changing water models (presumably that is what you mean, and just typoed it) will not work unless

[gmx-users] FFTW with AVX

Hi there, I just noticed that when I compile gromacs 5.1.1 with GMX_BUILD_OWN_FFTW=ON, it compiles fftw with avx support (at least that is what cmake reports: "The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2;--enable-avx"). However, in the

[gmx-users] Plumed-2.2.0 installation issue

Dear All, Lately, I am trying to install Plumed-2.2.0 in one system, the steps I follow, ./configure prefix=/home/tarak/software/plumed-2.2.0 CXX=mpicxx make install Config.log shows no error, but while giving "make install" it is coming out of the process with the following errors,

Re: [gmx-users] fix simulation box corners NVE

Hi Yuri, Sure. Which positions are used during the run and written out depends on the box and whether you use domain decomposition or not. Cheers, Tsjerk On Jan 4, 2016 11:15 PM, "Sereda, Yuriy Vladimirovich" wrote: > Thanks, this helps a bit, now I can be more specific:

Re: [gmx-users] Problem in Free Energy Calculations

Hi Justin.. Thanks a ton to you. Finally I have completed the simulation of ligand in solvent. In your earlier mail you have written that to calculate the binding energy of protein-ligand I will need the nonbonded interaction energy between protein-ligand coming from protein-ligand simulation and

Re: [gmx-users] Restarting Simulations

Thanks Justin for the input. Thanks, Soumya On Tue, Jan 5, 2016 at 8:55 AM, Soumya Lipsa Rath wrote: > Dear Gromacs Users, > > I am trying to restart a simulation using the following command > > gmx convert-tpr -s topol.tpr -nsteps 1 -o topol2.tpr > > mdrun_mpi

[gmx-users] draw histogram

hi gmx usersi am trying to plot histogram.xvg , but the graph isn't making any sense, or may be i dont understand it.in the gromacs tutorial from bevanlab (free energy calculations:methane) it says that we need to separate the data. how?  -- Gromacs Users mailing list * Please search the

Re: [gmx-users] Force-switch algorithm

Hi, On Tue, Jan 5, 2016 at 4:42 AM Pallavi Banerjee < pallavis...@students.iiserpune.ac.in> wrote: > Hi Mark, > > Thank you for your reply. > > I want to implement this wacky idea because a part of the potential of the > system needs to be input in a tabulated form (referring to Iterative >

Re: [gmx-users] fix simulation box corners NVE

Hi, And if you care, the solution is to post-process with trjconv, e.g. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. mdrun does whatever is computationally convenient, rather than speculating which representation people would like. Mark On Tue, Jan 5, 2016 at

[gmx-users] Protein-Protein distance

Dear Gromacs Users Kindly let me know how to calculate the protein protein distance as a function of time with gromacs. I want to calculate the distance based on the center of mass of the selection which is CA atoms. I have 4 proteins in the system and want to calculate the distances as distance

Re: [gmx-users] Force-switch algorithm

Hi Mark, I did go through the suggested section of the manual. I did not, however, come across any mention of using both tabulated and non-tabulated together. I don't see how that would be possible since the vdw-type and coulomb-type would take "User" as the parameter and no other, if I am to

[gmx-users] fix simulation box corners NVE

How to fix corners of the NVE or NVT Gromacs simulation box? How to transform existing trajectory to comply with this? How to set parameters of a new Gromacs simulation to make sure simulation box corners stay at fixed positions? Thanks, Yuri IU Bloomington Chemistry -- Gromacs Users

Re: [gmx-users] fix simulation box corners NVE

Hi Yuri, You have to distinguish between the systems lattice vectors and the positions of particles. The lattice remains fixed in NVE and NVT, but the particles are at many positions at the same time, and any position is good enough for putting in the XTC/TRR/GRO/PDB file. Hope it helps, Tsjerk

Re: [gmx-users] Scripts to the gromacs

On 1/4/16 6:09 PM, Elsaid Younes wrote: Hey all, I wish I can find a way to help me writing a script to the gromacs. I mean by scripts "the commands that one writes to gramacs terminals and the choices, which are prompted after command's processing, all collected in one file" I do simulation

Re: [gmx-users] Problem with editconf

I checked it. the pdb files are totally wrong but using vmd when i look at the gro files, all is well. On Mon, Dec 28, 2015 at 9:53 PM, Justin Lemkul wrote: > > > On 12/28/15 3:49 PM, abhishek khetan wrote: > >> Thanks for your reply again. Yes, it seems indeed a particularly

[gmx-users] Simulation of nonaqueous solvents

Is there a procedure/tutorial/method to calculate ssimulate ions in non-aqueous solvents from scratch? By "scratch" I mean that the the solvents I am trying to use (like dimethylsulfoxide or tetrahydrofuran or acetonitrile) and the ions ( Li+, Na+, etc )are way simpler than the huge protiens

[gmx-users] Implementing Gupta potential - different formulism

Dear All, I am looking at GROMACS for comparison to some DL_POLY results, in which a metal nanoparticle is heated in the NVT ensemble. However, the potential used is the Gupta potential, which has different terms to the generic model presented in the manual. Is there any way of implementing

Re: [gmx-users] Force-switch algorithm

Hi, On Mon, Jan 4, 2016 at 9:48 AM Pallavi Banerjee < pallavis...@students.iiserpune.ac.in> wrote: > Thank you for your reply, Mark! I have now thought of modifying my input > potential, that is, making changes to the tabulated form of potential. Yes, this is what you need to do if somehow you

Re: [gmx-users] Simulation of nonaqueous solvents

On 1/4/16 12:56 PM, abhishek khetan wrote: Is there a procedure/tutorial/method to calculate ssimulate ions in non-aqueous solvents from scratch? By "scratch" I mean that the the solvents I am trying to use (like dimethylsulfoxide or tetrahydrofuran or acetonitrile) and the ions ( Li+, Na+,