[gmx-users] NPT simulation stage

hi GMX users please help me i want to simulate protein-ligand complex by gromacs4.6.5 when i repeat NPT simulation stage  many times,  simulation results are very different for the pressure average.I sincerely thank you for your guidance -- Gromacs Users mailing list * Please search the archive

Re: [gmx-users] High Pressure with Martini system

Hi Ricardo, Insanely built systems with polarizable watets may be tricky, especially if the system is large (not to say humongous). Maybe it's worth adding a stage using normal Martini water, let that equilibrate (NVT and NpT), and then add in the polarizable sites, letting the system equilibrate

Re: [gmx-users] High Pressure with Martini system

On 25.04.2014 00:07, Ricardo O. S. Soares wrote: I ran an NVT equilibration of a 24mi CG Martini atoms and detected the formation of vacuum spots on the solvent. CG Martini has many sphere types, did you solvate your system with 24x10^6 MARTINI-W segments? MARTINI-W is is strongly association

[gmx-users] High Pressure with Martini system

Dear colleagues, I ran an NVT equilibration of a 24mi CG Martini atoms and detected the formation of vacuum spots on the solvent. However, the log file shows a very large negative pressure (about -4e+28) all the time, since the beginning. Despite the negative pressure, when I turn pressure co

Re: [gmx-users] how to manipulate solute-solvent interactions in ff to get the correct solvation free energy?

On 4/24/14, 3:48 PM, Golshan Hejazi wrote: Dear all, I have computed the solvation free energy of a molecule in a non aqueous solvent using thermodynamics integration in gromacs. The value is negative and high (-70kj/mol). The experimental value is almost -52kj/mol. From the output of TI,

Re: [gmx-users] skipping the EM, NPT and NVT for re-run

Please keep the discussion on the mailing list. On 4/24/14, 4:29 PM, Saman Shahriyari wrote: you mean i should expect a different trajectory every time i do the simulation under the same conditions?! It's certainly possible. http://www.gromacs.org/Documentation/Terminology/Reproducibility O

[gmx-users] how to manipulate solute-solvent interactions in ff to get the correct solvation free energy?

Dear all, I have computed the solvation free energy of a molecule in a non aqueous solvent using thermodynamics integration in gromacs. The value is negative and high (-70kj/mol). The experimental value is almost -52kj/mol.  >From the output of TI, there exist a lambda value which correspond to

[gmx-users] compilation issues with GCC/clang/CUDA on OSX

Hello - I am trying to compile gromacs 4.6.5 with CUDA support for a new graphics card on OSX 10.8.5 with CUDA 6.0.37 using gcc 4.8.2 from fink (gcc-4 and g++-4) for OpenMP support and clang for CUDA as recommended previously. I am starting cmake like this: export CC=/sw/bin/gcc-4 export CXX=/sw

Re: [gmx-users] make install creating infinite recursive directories: addendum

BS"D Dear Mark, Thanks for your reply. I initially tried it without the trailing slash (i.e., "/share/apps/gromacs-4.6.5") with the same effect. I am using the tar file downloaded from the gromacs web site. Did you try this on Centos 6.5? Thanks Harry Harry M. Greenblatt Associate Sta

Re: [gmx-users] make install creating infinite recursive directories: addendum

Hi, That makes no sense. I can't reproduce your symptoms at all (with git version or tarball). The build system does append "/" and then "share/gromacs" to CMAKE_INSTALL_PREFIX before using it for the files in the top directory, but there's no conceivable way the build system could spam successive

Re: [gmx-users] Com pulling in reverse Z direction in SMD simulation..

Thank you Justin. I got the point. Whatever you have replied those were my query. Actually I could not able to push the drug molecule to the active site and md run was finished normally without any error. Thank you once again Justin On Thu, Apr 24, 2014 at 8:35 PM, Justin Lemkul [via GROMACS]

Re: [gmx-users] QM/MM simulations

On 4/24/14, 12:28 PM, Iamkaant wrote: Thanks for rapid answer! I'm willing to try the latest version with your patch. But since I'm quite new to Linux, I'll be very thankful if you explain me how to use gromacs git server, and apply patches. (where to download the source code and the patch) h

Re: [gmx-users] QM/MM simulations

Thanks for rapid answer! I'm willing to try the latest version with your patch. But since I'm quite new to Linux, I'll be very thankful if you explain me how to use gromacs git server, and apply patches. (where to download the source code and the patch) Sincerely, Andrey. -- View this message in

Re: [gmx-users] Com pulling in reverse Z direction in SMD simulation..

On 4/24/14, 10:46 AM, Kalyanashis wrote: Thank you Justin.. I have done the calculation with "pull_vec1= 0.0 0.0 1 " option but do not get the expected result. Actually, I want to push the drug molecule to its initial position i.e. after pulling it has come out from the active site of the enzym

Re: [gmx-users] QM/MM simulations

On 4/24/14, 9:34 AM, Iamkaant wrote: Dear Justin! I'm very sorry to waste your time, but I've got an issue with ORCA support in GROMACS and hope you can help me. I'm installing gromacs-4.6.5 on my Dell PowerEdge R720 machine running Suse 12.3 x64 ( 3.7.10-1.28-desktop core). Installed version o

Re: [gmx-users] Com pulling in reverse Z direction in SMD simulation..

Thank you Justin.. I have done the calculation with "pull_vec1= 0.0 0.0 1 " option but do not get the expected result. Actually, I want to push the drug molecule to its initial position i.e. after pulling it has come out from the active site of the enzyme now I want to push it to the active site. P

Re: [gmx-users] QM/MM simulations

Dear Justin! I'm very sorry to waste your time, but I've got an issue with ORCA support in GROMACS and hope you can help me. I'm installing gromacs-4.6.5 on my Dell PowerEdge R720 machine running Suse 12.3 x64 ( 3.7.10-1.28-desktop core). Installed version of ORCA is orca_3_0_0_linux_x86-64. 0)Prev

[gmx-users] make install creating infinite recursive directories: addendum

BS"D I just tried to build gromacs on a workstation with Centos 6.5, under /opt and got the same problem. So it's not a ROCKS issue. I *did* succeed on a Centos 6.5 workstation where I *didn't* specify the CMAKE_INSTALL_PREFIX and "make install" put things in /usr/local. Thanks Harry Hi A

Re: [gmx-users] Cannot write trajectory frame; maybe you are out of disk space

You've been reading a bit selectively. I asked if you're trajectories wrote any output at all, but you haven't said. If, as I've already said, you know you were able to write output because gmxcheck says there's content in the files, then a flaky network file system is likely. But you haven't given

Re: [gmx-users] Com pulling in reverse Z direction in SMD simulation..

On 4/24/14, 5:21 AM, Kalyanashis wrote: Dear all, I am doing SMD simulation of a enzyme system and I have given the pull option in Z direction. The com pulling options are given below, ;COM pulling pull = umbrella pull_geometry= distance pull_dim

[gmx-users] make install creating infinite recursive directories

BS"D Hi All, I am trying to build 4.6.5 for testing, on a Rocks 5.3 cluster (yes it needs upgrading!). I am using one of the compute nodes to do the compiling, using the following: CMAKE_PREFIX_PATH=/share/apps/fftw-3.3.2 /share/apps/cmake-2.8.12.2/bin/cmake .. -DCMAKE_INSTALL_PREFIX=/sha

[gmx-users] Cannot write trajectory frame; maybe you are out of disk space

Dear Mark I corrected file permission in my system using chmod -R 777 . But I encountered the same error: File input/output error: Cannot write trajectory frame; maybe you are out of disk space. Any help will highly appreciated -- Gromacs Users mailing list * Please search the archive at htt

[gmx-users] Com pulling in reverse Z direction in SMD simulation..

Dear all, I am doing SMD simulation of a enzyme system and I have given the pull option in Z direction. The com pulling options are given below, ;COM pulling pull = umbrella pull_geometry= distance pull_dim = N N Y pull_r1 = 1 pull

Re: [gmx-users] Non-neutral system

Dear Carsten, I studied your interesting article. The maximum of positive charge in my simulation box is about +40e and interface of CO2 with water. The cations can be located at the interface. I have a question, if I choose the explicit uniform background charge approach, can it make sense? I c

Re: [gmx-users] Special bond between metallic layers & protein

Ah, I have to write down the old residue instead of leaving the spaces blank! Like this for a toy pdb file with only 2 platinum atoms it work ;) meaning that the matrix of the distances between all the special atoms is constructed, the special atom around the cut-off distance are linked and no erro

[gmx-users] normal mode analysis - regd

Dear Gromacs users, I am performing normal mode analysis (NMA) for a crystal, but in the vibrational spectrum that obtained from NMA, there are no low frequency lattice modes ( i.e., no peaks in spectrum below 50 cm-1). But the spectrum that have obtained from velocity auto correl

Re: [gmx-users] Special bond between metallic layers & protein

Dear Mark, thank you very much for your reply. I do this and then I define the same bonds for PT2 as for PT1 (which of course sounds redundant, but I had read Manual 5.6.7 and if I do not rename the residue I get the following message: *Invalid line 'PT PT 1 PT PT1