[gmx-users] PBC problem in bilayer system

Dear Michael Carter Thanks for your answer. I used -pbc nojump Followed by -fit rot+trans Unfortunately, my problem was not solved. Please guide me to solve this problem. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Lis

Re: [gmx-users] use of " -t nvt.cpt" option in NPT equilibration

Hi Ansuman, With -t nvt.cpt the positions, velocities and other state information is taken from the .cpt file. Otherwise, the positions and velocities are taken from the lower precision .gro file, and other state information is not available. Adding -t nvt.cpt will result in a more exact continuat

[gmx-users] Contact angle measurement on a flat surface

Dear all,I would like to know what are the methods I could use to measure/plot the contact angle of a water nanodroplet on flat graphene.Is there a script or tool in GROMACS that can perform the contact angle calculation? I am aware that the commonly used Young's equation does not apply here, since

Re: [gmx-users] g_mindist for hydrophobic interactions

  you should go down the list and use all the tools, and use some from seperate software.  In my experience, the trjconv gets rid of say 4-5 crazy single points in a graph based on a single point where one of the atoms or residues involved moves between planes, which averidge out in a gaussian dis

Re: [gmx-users] protein-ligand complex by gromacs

did you center everything, or are you just looking at it in VMD?   Gesendet: Montag, 08. September 2014 um 18:30 Uhr Von: "Mahboobeh Eslami" An: "gmx-us...@gromacs.org" Betreff: [gmx-users] protein-ligand complex by gromacs hi GMX users i have simulated the protein-ligand complex by gromacs.

Re: [gmx-users] g_energy reporting 0.0000 interaction energy between energy groups in GPU run?

Thank you for your quick answer, Justin. I'll make new .edr files using only CPUs. Best regards, Leandro On Tue, Sep 9, 2014 at 10:11 PM, Justin Lemkul wrote: > > > On 9/9/14 9:09 PM, Leandro Bortot wrote: > >> Dear users, >> >> I did some simulations of organic molecules in solution to

Re: [gmx-users] g_energy reporting 0.0000 interaction energy between energy groups in GPU run?

On 9/9/14 9:09 PM, Leandro Bortot wrote: Dear users, I did some simulations of organic molecules in solution to study how they interact, but I'm facing some problems and your help would be greatly appreciated. Consider the following case: I simulated two copies of molecule "AcO" st

[gmx-users] g_energy reporting 0.0000 interaction energy between energy groups in GPU run?

Dear users, I did some simulations of organic molecules in solution to study how they interact, but I'm facing some problems and your help would be greatly appreciated. Consider the following case: I simulated two copies of molecule "AcO" starting from a structure in which they are non-c

Re: [gmx-users] Cuda CC 2.0 restrictions

On Tue, Sep 9, 2014 at 10:58 PM, Mirco Wahab wrote: > Thank you very much for your answer. After reading > Mark's very detailed posting on the topic, I played > with some parameters but did not manage to get under > 64K grid dimension. > > On 09.09.2014 21:35, Szilárd Páll wrote: >> >> Is this rat

Re: [gmx-users] Using GROMACS to find the net charge on a Protein

Quick answer is no. In fact, that's really not what (standard) molecular dynamics is for. You need a constant-pH MD method for that. Read this to get a bit more acquainted with the subject (might be overkill for you, because I doubt this is what you want/need): http://www.gromacs.org/Documentatio

Re: [gmx-users] Using GROMACS to find the net charge on a Protein

On 9/9/14 3:51 PM, Agnivo Gosai wrote: Dear Users I am trying to find the net charge at the physiological pH value for a protein molecule (Thrombin) in my case and am wondering if it is possible to use GROMACS for doing it. I am very new to GROMACS and at present I have been going through the

Re: [gmx-users] use of " -t nvt.cpt" option in NPT equilibration

On 9/9/14 5:09 PM, R.S.K.Vijayan wrote: Hi Ansuman, That is optional. Generally speaking, no, it's not. The real truth lies in what the .mdp settings are and what the intent of NPT is. If you don't pass the .cpt file to grompp -t, you stand to lose much (or all) of the previous state in

Re: [gmx-users] use of " -t nvt.cpt" option in NPT equilibration

Hi Ansuman, That is optional. Regards, Vijayan.R On Tue, Sep 9, 2014 at 4:38 PM, Ansuman Biswas < ansu...@physics.iisc.ernet.in> wrote: > Hi, > Can someone please explain if it is necessary to use the -t flag during > NPT equilibration? > > The following command is mentioned in the lysozyme

[gmx-users] use of " -t nvt.cpt" option in NPT equilibration

Hi, Can someone please explain if it is necessary to use the -t flag during NPT equilibration? The following command is mentioned in the lysozyme tutorial: $ grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr whereas , I have found the command without the -t flag in another tutoria

Re: [gmx-users] Cuda CC 2.0 restrictions

Thank you very much for your answer. After reading Mark's very detailed posting on the topic, I played with some parameters but did not manage to get under 64K grid dimension. On 09.09.2014 21:35, Szilárd Páll wrote: Is this rather large box a system that can actually be simulated with a useful

[gmx-users] Using GROMACS to find the net charge on a Protein

Dear Users I am trying to find the net charge at the physiological pH value for a protein molecule (Thrombin) in my case and am wondering if it is possible to use GROMACS for doing it. I am very new to GROMACS and at present I have been going through the tutorials by Dr. Lemkul. I have seen that

Re: [gmx-users] Cuda CC 2.0 restrictions

Hi, Is this rather large box a system that can actually be simulated with a useful speed on a single Fermi GPU? Even with 5 fs time-step you won't get much more than 1-1.5 ns/day on a fast Fermi GPU like a GTX 580. Given that you are quite a bit above the limit, unless you are using a quite large

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 125, Issue 20

Thank you very much! Sincerely nil On Thu, Sep 4, 2014 at 2:51 PM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit

Re: [gmx-users] Query regarding the addition of solvent molecule

On 9/9/14 9:41 AM, Christina Florina wrote: Hi, Thank you for the suggestions. I did the modifications in the .itp file and the grompp step generated the .tpr file successfully. But now, I am facing problem in the genion step, while adding the NA ions the group 13 (usually SOL for w

Re: [gmx-users] PBC problem in bilayer system

Also if you want to fix the position on the centre of mass (no rotating or translating) try -pbc nojump Followed by -fit rot+trans Remember to use you new .xtc from your no jump command for the -fit command. Then view in vmd and your molecules will not jump, rotate, or translate around the box.

Re: [gmx-users] PBC problem in bilayer system

Hi, Try -pbc nojump Best, Mike On 09/09/2014 15:11, "shahab shariati" wrote: >Dear gromacs users > >I did MD simulation of my system containing DPPC lipids + water molecule >and 4 drug molecules. > >I saw trajectory file using VMD. > >Unfortunately, drug molecules jump across the box. > >How t

[gmx-users] PBC problem in bilayer system

Dear gromacs users I did MD simulation of my system containing DPPC lipids + water molecule and 4 drug molecules. I saw trajectory file using VMD. Unfortunately, drug molecules jump across the box. How to resolve this PBC problem? which of -pbc options (none, mol, res, atom, nojump, cluster or

[gmx-users] mean-square displacement

Hello all I would like to plot mean square displacement of hydrogen atoms of protein versus temperature (in order to get dynamical transition temperature). I am using g_msd for this purpose (g_msd -f *_nopbc.xtc -s *.tpr -n index.ndx -o *.xvg) . I am getting following curves as uploded in : http:

Re: [gmx-users] Query regarding the addition of solvent molecule

Hi, Thank you for the suggestions. I did the modifications in the .itp file and the grompp step generated the .tpr file successfully. But now, I am facing problem in the genion step, while adding the NA ions the group 13 (usually SOL for water solvent) is not present there. If I select an

Re: [gmx-users] Gromacs 5.0 compilation slower than 4.6.5. What wentwrong ?

Thank you very much to all of you. That should explain the difference in performance. I'll also discuss it with a more gromacs-knowledgeable colleague of mine. Best Regards. 2014-09-06 8:58 GMT+02:00 Abhi Acharya : > Thank you Mark and Szilard for your replies. It gave more clarity on how > the

[gmx-users] mean square displacement

Hello all I would like to plot mean square displacement of hydrogen atoms of protein versus temperature (in order to get dynamical transition temperature). I am using g_msd for this purpose (g_msd -f *_nopbc.xtc -s *.tpr -n index.ndx -o *.xvg) . I am getting following curves as uploded in : http:

Re: [gmx-users] Modifying the protein chain in GROMACS

On 9/9/14 8:51 AM, Tim Stauch wrote: Dear all, I am currently trying to “mutate" a protein by changing its backbone directly, i.e. I am not interested in changing a specific amino acid against another (I’ve found out that you can use VMD or Pymol for this purpose), but I am rather intereste

[gmx-users] Modifying the protein chain in GROMACS

Dear all, I am currently trying to “mutate" a protein by changing its backbone directly, i.e. I am not interested in changing a specific amino acid against another (I’ve found out that you can use VMD or Pymol for this purpose), but I am rather interested in changing certain atoms in the backbo

Re: [gmx-users] Query regarding the addition of solvent molecule

On 9/9/14 7:09 AM, Christina Florina wrote: Hi, Thanks for your suggestions. If the .itp file has error, is there any other way to generate .itp files for the solvents or do i need to write them manually? Because the .itp files I have attached are generated using PRODRG. If I edit t

Re: [gmx-users] Query regarding the addition of solvent molecule

Hi, Thanks for your suggestions. If the .itp file has error, is there any other way to generate .itp files for the solvents or do i need to write them manually? Because the .itp files I have attached are generated using PRODRG. If I edit the chx.itp file based on the corrections you have

[gmx-users] Postdoc Position Available

A postdoctoral position in computational physics of Carbon Nano Tubes (CNTs) is available at Khalifa University, Abu Dhabi, UAE.The successful candidate will work in a highly collaborative environment with experimental and theoretical scientist. The candidate should have a good knowledge of Mol

Re: [gmx-users] Query regarding the addition of solvent molecule

On 9/9/14 12:51 AM, Christina Florina wrote: Hi, I have included the link to my dropbox where I have attached my gromacs topology files. Though I have included the cyclohexane itp file in the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO, Kindly need help in this regar

[gmx-users] Spherical Position Restrain from the center of the Box

Dear gromacs user: I plan to do a coarse grain simulation for a whole virus coat. It only contains virus surface protein, so I'm afraid it will collapse due to lack of inner member lipids. I plan to add a Spherical Position Restrain from the center of the Box, to prevent the surface protein fa

[gmx-users] PBC only on x and y in an NPT ensemble

Dear all I would like to simulate coarse grained thin polymer films supported on a wall or a substrate (I don't really mind) but with the one interface to be free. I would like to do this under NPT conditions. I would expect that this can only be done by putting pbc=xy, as in the to the following

Re: [gmx-users] GPU job failed

I recompiled Gromacs-5.0.1, finally it works now Probably I made some mistakes in previous compiling thanks a lot guys regards Albert On 09/09/2014 09:16 AM, Carsten Kutzner wrote: Hi, from the double output it looks like two identical mdruns, each with 1 PP process and 10 OpenMP thr

Re: [gmx-users] GPU job failed

thank you for reply. I compiled it with command: env CC=mpicc CXX=mpicxx F77=mpif90 FC=mpif90 LDF90=mpif90 CMAKE_PREFIX_PATH=/home/albert/install/intel-2013/mkl/include/fftw:/home/albert/install/intel-mpi/bin64 cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=/home/

Re: [gmx-users] GPU job failed

thank you for reply. I compiled it with command: env CC=mpicc CXX=mpicxx F77=mpif90 FC=mpif90 LDF90=mpif90 CMAKE_PREFIX_PATH=/home/albert/install/intel-2013/mkl/include/fftw:/home/albert/install/intel-mpi/bin64 cmake .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF -DCMAKE_INSTALL_PREFIX=/home/

Re: [gmx-users] GPU job failed

Hi, from the double output it looks like two identical mdruns, each with 1 PP process and 10 OpenMP threads, are started. Maybe there is something wrong with your MPI setup (did you by mistake compile with thread-MPI instead of MPI?) Carsten On 09 Sep 2014, at 09:06, Albert wrote: > Here ar

Re: [gmx-users] GPU job failed

Here are more informations from log file: mpirun -np 2 mdrun_mpi -v -s npt2.tpr -c npt2.gro -x npt2.xtc -g npt2.log -gpu_id 01 -ntomp 0 Number of hardware threads detected (20) does not match the number reported by OpenMP (10). Consider setting the launch configuration manually! Number of hardw