[gmx-users] Regarding installation problem

Hi I have found the following problem regarding gromacs 5.1.2 installation. I have installes cmake and ffftw before. Can you help me out? -- Configuring incomplete, errors occurred! See also "/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeOutput.log". See also

[gmx-users] Mdrun with rdd option

Dear Gromacs users, I am trying to run a simulation but I am getting the error regarding the domain decomposition. I ran the simulation using "rdd" option and it is running fine. Kindly tell me whether "-rdd" option will affect my simulation. If yes, then which values would get affected using

[gmx-users] Huge conformational change of ATP molecules

Hi Gromacs Users, I'm running 20ns MD simulation of a protein kinase with ATP bond. I use amber99sb-ildn force field with parameters of ATP derived from the database of Richard Bryce. What surprised me is that the ATP molecules displays a huge flexibility and conformational change. First, it

Re: [gmx-users] confusion on energy for a system of protein sovated in water

Thanks Justin, How about LJ and Coulomb energy? I want to see the trend of protein energy only. I defined 2 energy group: protein and SOL in .mdp file. Then, I saw LJ and Coulomb: protein-ptrotein option when using g_energy. Are they VDW and Coulomb force within the protein only? --

Re: [gmx-users] confusion on energy for a system of protein sovated in water

On 2/22/16 8:33 PM, Ming Tang wrote: Dear lists, After pulling a protein in water and performing mdrun -rerun, I found that G96Bond, G96Angle, COM-Pull-En and Potential energy extracted from the original system using g_energy -f ener.edr , and from the -rerun system using g_energy -f

[gmx-users] confusion on energy for a system of protein sovated in water

Dear lists, After pulling a protein in water and performing mdrun -rerun, I found that G96Bond, G96Angle, COM-Pull-En and Potential energy extracted from the original system using g_energy -f ener.edr , and from the -rerun system using g_energy -f rerun.edr have different values. Firstly, are

Re: [gmx-users] fix COM

On 2/22/16 8:24 PM, Ming Tang wrote: Hi Mark, When I submitted my job to our HPC sever, I got this error message: gromacs/5.0.4(14):ERROR:151: Module 'gromacs/5.0.4' depends on one of the module(s) '' gromacs/5.0.4(14):ERROR:102: Tcl command execution failed: prereq mpt/2.10 I have been

Re: [gmx-users] fix COM

Hi Mark, When I submitted my job to our HPC sever, I got this error message: gromacs/5.0.4(14):ERROR:151: Module 'gromacs/5.0.4' depends on one of the module(s) '' gromacs/5.0.4(14):ERROR:102: Tcl command execution failed: prereq mpt/2.10 I have been told that the mpt version has been updated

Re: [gmx-users] Extend the simulation

Hi, I have two inquiries: 1-I got this error message: Fatal error: Checksum wrong for 'md_0_1.log'. The file has been replaced or its contents have been modified. Cannot do appending because of this condition. For more information and tips for troubleshooting, please check the GROMACS website at

Re: [gmx-users] Embedding Protein into lipid bilayer

On 2/22/16 4:40 AM, khourshaeisha...@mech.sharif.ir wrote: Dear Justin Thanks for your reply. I think, I got what you mean. By the way, My protein needs to use BGL residue and of course this type of the residue isnt available in the gromacs sources. So I find its

Re: [gmx-users] Potential energy

On 2/21/16 3:35 PM, mohammad r wrote: Thank you Justin, do you know how I can find or modify the center of mass velocity of my system? During the run? If using comm-grps (you should for any system with PBC), then the COM velocity should be kept at or close to zero. You can confirm after

Re: [gmx-users] OpenCL compile error

; wrote: > > > > > Dear GMX users, > > > > > > When I try to run a simulation, I get the following error: > > > > > > Selecting kernel for AMD > > > The OpenCL compilation log has been saved in > > "nbnxn_ocl_kernels.cl.FAILED" > > > > > > --

Re: [gmx-users] OpenCL compile error

ijk.info> > wrote: > > > Dear GMX users, > > > > When I try to run a simulation, I get the following error: > > > > Selecting kernel for AMD > > The OpenCL compilation log has been saved in > "nbnxn_ocl_kernels.cl.FAILED" > > &g

[gmx-users] Beginner's problem: g_rdf functions and -com

Dear Gromacs users, This is my first time writing to this mailing list. I am writing in order to inquire about something which is after reading the manual quite extensively still unclear for me. I will explain my problem in detail, including details about my simulation. I hope you do not get

Re: [gmx-users] OpenCL compile error

t the following error: > > > > Selecting kernel for AMD > > The OpenCL compilation log has been saved in > "nbnxn_ocl_kernels.cl.FAILED" > > > > --- > > Program: gmx mdrun, version 2016-dev-20160222-29943f

Re: [gmx-users] OpenCL compile error

> Selecting kernel for AMD > The OpenCL compilation log has been saved in "nbnxn_ocl_kernels.cl.FAILED" > > --- > Program: gmx mdrun, version 2016-dev-20160222-29943fe > Source file: src\gromacs\mdlib\nbnxn_ocl\nbnxn_oc

[gmx-users] OpenCL compile error

Dear GMX users, When I try to run a simulation, I get the following error: Selecting kernel for AMD The OpenCL compilation log has been saved in "nbnxn_ocl_kernels.cl.FAILED" --- Program: gmx mdrun, version 2016-dev-20160222-2994

Re: [gmx-users] how to correct/remove error installation issue

Dear Mehreen, You need to recompile. How was your gromacs installed the first time around? The error basically tells you to issue "cmake -DGMX_USE_RTD SCP=OFF " at the cmake step. Kind regards, Erik > On 22 Feb 2016, at 15:04, Mehreen Jan wrote: > > > thank you!

[gmx-users] how to correct/remove error installation issue

thank you! Erik any idea how to fix this error?? version 5.0.7 this is not a space issue i think it is installation issue any idea how to fix this issue??? thank you > > > error: > > the gmx executable was compiled to use the rdtscp CPU > > instruction. however  this is not supported by

Re: [gmx-users] fix COM

Hi, On Mon, Feb 22, 2016 at 2:10 AM Ming Tang wrote: > Thank you Mark, > > Could you please help to give more instructions on how to generate > restraints on a centre of mass virtual site? I know genrestr can implement > restraints, but I have no idea how to set a virtual

Re: [gmx-users] Did not find any molecules of type ...

Hi, That means there's two definitions of a WAT [moleculetype]. You need to find both in your set of #included files, and work out where the error lies. Mark On Mon, Feb 22, 2016 at 1:55 PM Marta Wisniewska < marta.d.wisniew...@gmail.com> wrote: > Hello Justin, > > my topology file: >

Re: [gmx-users] Did not find any molecules of type ...

Hello Justin, my topology file: WAT_GMX.top created by acpypi on Tue Mar 3 13:26:34 2009 ; Include forcefield parameters #include "amber99sb-star-ildnp.ff/forcefield.itp" [ moleculetype ] ;molname nrexcl WAT 2 [ atoms ] ; id at type res nr res name at name cg nr

[gmx-users] Embedding Protein into lipid bilayer

Dear Justin Thanks for your reply. I think, I got what you mean. By the way, My protein needs to use BGL residue and of course this type of the residue isnt available in the gromacs sources. So I find its information in ATP site and it is attached to my Email as a .itp file.