Re: [gmx-users] LINCS warming, but continued EM

Dear Justin, Thank you very much for your all helps. (1) How can I easily reduce these clashes? Is there any good software? (2) from geometrical view, EM.gro structure looks fine. However, there are many individual protons separated from Lipid molecules. Is this usual? Best regards,

[gmx-users] nvidia tesla p100

Hi, I was wondering, does Gromacs support nVidia Tesla P100 cards? I’m trying to run a simulation on a node with this GPU, but whatever I tried, I can’t get Gromacs to detect a cuda-capable card: NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not

Re: [gmx-users] nvidia tesla p100

Hi, Sure, any CUDA build of GROMACS will run on such a card, but you want 2016.1 for best performance. Your problem is likely that you haven't got a suitably new driver installed. What does nvidia-smi report? Mark On Sun, Oct 30, 2016 at 1:13 AM Irem Altan wrote: > Hi, >

[gmx-users] Orienting molecule in a correct direction

Dear all, I want to define z axis as the reaction coordinate in a series of umbrella sampling simulations. As a first step, I use the editconf -prince to orient the ligand along the x axis and then I change the x and z columns in an editor. But, every time I get error at pulling step. Could you

Re: [gmx-users] Orienting molecule in a correct direction

On 10/30/16 12:03 AM, faride badalkhani wrote: Dear all, I want to define z axis as the reaction coordinate in a series of umbrella sampling simulations. As a first step, I use the editconf -prince to orient the ligand along the x axis and then I change the x and z columns in an x and z

Re: [gmx-users] pmf

On 10/28/16 4:20 PM, Alex wrote: Thanks for your response. The version for all tasks is "gmx, VERSION 5.1.2". I hope extra windows would be required just in the gaps, not in the whole reaction path. Yes, you just need more windows. I had 81 windows spacing mostly 0.01 nm and in the end

Re: [gmx-users] HELP：how could the simulation restarted from md*_prev.cpt rather than the md*.cpt

On 10/28/16 11:23 PM, 张慧玲 wrote: Hi, Justin I have 17 replicas, so I got {md0.cpt,md0_prev.cpt}, ..{md16.cpt,md16_prev.cpt}. Then I told gromacs to restart from the _prev.cpt using the following command: mpirun -np 17 mdrun -deffnm md -multi 17 -noddcheck -replex 5 -nsteps

Re: [gmx-users] LINCS warming, but continued EM

On 10/29/16 7:44 AM, Mijiddorj Batsaikhan wrote: Dear Justin, Thank you very much for your all helps. (1) How can I easily reduce these clashes? Is there any good software? You're using it. The point of energy minimization is to relax the structure. It just so happens that you have some

Re: [gmx-users] Md simulation error

On 10/29/16 5:04 AM, maria khan wrote: Thanks alot Justin A. Lemkulfor your strong concern. can you please guide me in conforming protonation states for residues.im new user of gromacs for simulation. Start with some basic tutorials that show you how everything works in good systems.

[gmx-users] Md simulation error

Thanks alot Justin A. Lemkulfor your strong concern. can you please guide me in conforming protonation states for residues.im new user of gromacs for simulation. Regards. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List