Re: [gmx-users] problem with gmx genconf?

I'm sorry Dr. Lemkul. I thought I put the links for the images I uploaded on Google Drive. Let me try it again. The single molecule: https://drive.google.com/open?id=0B3dugKVFN2ajTmZMYVdOX0NfbGM The system that was generated by

[gmx-users] Multithread run issues

Hi, Users issue the command "mdrun -v" and that will automatically read input files in the working directory. There are two issue with that which I am not aware of the solution. 1- How the number of cores can be changed? 2- Viewing the output of "top" command, it is saying that mdrun uses 400%

Re: [gmx-users] principal component analysis chain break (Tsjerk Wassenaar)

Dear Tsjerk， I visually checked the trajectory(md_backbone.xtc) in VMD and there is no break. Actually I spelled wrong that md1_backbone.xtc and md_backbone.xtc is the same. Best regards, Jie -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] gromacs build options

Hi, Great. But CMAKE_INSTALL_PREFIX and CMAKE_PREFIX_PATH are different things that do different jobs (specify where to install vs where to search for dependencies). Mark On Sun, Oct 9, 2016 at 12:20 PM Mahmood Naderan wrote: > Hi mark, > Thank you very much. In fact the

Re: [gmx-users] gromacs build options

Thanks. Got it. Regards, Mahmood On Sun, Oct 9, 2016 at 2:36 PM, Mark Abraham wrote: > Hi, > > Great. But CMAKE_INSTALL_PREFIX and CMAKE_PREFIX_PATH are different things > that do different jobs (specify where to install vs where to search for > dependencies). > >

Re: [gmx-users] Multithread run issues

Hi, On Sun, Oct 9, 2016 at 2:06 PM Mahmood Naderan wrote: > Hi, > > Users issue the command "mdrun -v" and that will automatically read input > > files in the working directory. There are two issue with that which I am > > not aware of the solution. > > > > 1- How the

Re: [gmx-users] problem with gmx genconf?

On 10/9/16 9:22 PM, Thejus Kartha wrote: Well, the literature reports a non-zero dipole moment and hence, a polarity index of 4.8 for 1,4-dioxane. So does the organic chemist nearby. I'm not sure if I understand your perspective, Dr. Lemkul. I'm clearly missing something here. It's a

[gmx-users] problem encountered during installation, the AVX2_256support

Dear gmx users: I encountered a problem when I was installing the gromacs. I used "cmake .. -DGMX_SMID=AVX2_256" command try to support my new intel CPU,but the system reports the following things: -- Compiler flag was valid, but executable did not build - perhaps update the

Re: [gmx-users] problem with gmx genconf?

Well, the literature reports a non-zero dipole moment and hence, a polarity index of 4.8 for 1,4-dioxane. So does the organic chemist nearby. I'm not sure if I understand your perspective, Dr. Lemkul. I'm clearly missing something here. I should also mention that I have run simulations of

[gmx-users] problem with gmx genconf?

Greetings, all.I have been trying to perform a simulation using the following solvent (1,4-dioxane) molecule: Screenshot from 2016-10-10 05-11-13.png | | | | || | | | || Screenshot from 2016-10-10 05-11-13.png | | | | The .gro file corresponding to

Re: [gmx-users] PMF and lack if NPT equilibration

On 10/8/16 2:46 PM, Alex wrote: Dear gromacs user, In a PMF simulation of a short peptide on solid surface, I am using the "direction-periodic" as "pull-coord1-geometry" in the Z direction, then as you know the equilibration of the system in NPT ensemble is not doable for the individual

Re: [gmx-users] problem with gmx genconf?

None of your screenshots work; most users receive mail in plain text. If you want to share files or images, upload them somewhere and provide a link. [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB ; residue 903 DOX rtp DOX q

Re: [gmx-users] problem with gmx genconf?

On 10/9/16 8:26 PM, Thejus Kartha wrote: I'm sorry Dr. Lemkul. I thought I put the links for the images I uploaded on Google Drive. Let me try it again. The single molecule: https://drive.google.com/open?id=0B3dugKVFN2ajTmZMYVdOX0NfbGM The system that was generated by

Re: [gmx-users] gromacs build options

Hi mark, Thank you very much. In fact the following commands did the job $ cmake .. -DCMAKE_C_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpicc -DCMAKE_CXX_COMPILER=/share/apps/computer/openmpi-2.0.1/bin/mpic++ -DCMAKE_PREFIX_PATH=/share/apps/chemistry/gromacs-5.1 -DGMX_BUILD_OWN_FFTW=ON