Re: [gmx-users] Fwd: how to get .mdp files

mdp file is parameter file for md simulations. You need to copy if you want to use the parameters used in the tutorial. You can also change that parameter according to your use and need. On Sat, Feb 17, 2018 at 7:34 AM, neelam wafa wrote: > -- Forwarded message

[gmx-users] Fwd: how to get .mdp files

-- Forwarded message -- From: "neelam wafa" Date: 17 Feb 2018 00:57 Subject: how to get .mdp files To: Cc: Hi I am new to this list. I have run the gromacs tutorial ' lysosime in water'. now i have to run a

[gmx-users] Print neighbour list

Hi, I am trying to output the neighbor list calculated during a simulation. I consulted the manual which says that DUMPNL is the env variable suited for this purpose. In my bash script I first set up: export DUMPNL=10 and then run the simulation (GROMACS version 4.5.4). I do not see any

[gmx-users] ion channel in lipid bilayer

Hi all! I have a question concerning immersion of the ion channel (four subunits with extracellular domains and a bundles of helixes) into the lipid bilayer. 6 years ago I used some tutorial or mailing lists, which described the way from KALP15 tutor. With CCR5 model there were no problems at

Re: [gmx-users] Problems with trjconv

On 2/16/18 3:00 PM, Poncho Arvayo Zatarain wrote: Where shud i see the answer Justin? Please tell me Like any other post, in your email. -Justin De: gromacs.org_gmx-users-boun...@maillist.sys.kth.se en

Re: [gmx-users] GPU problem with running gromacs.2018

Hi, You can upload a log file to a file-sharing service and share the link :-) Mark On Fri, Feb 16, 2018 at 8:22 PM Osmany Guirola Cruz < osmany.guir...@biocomp.cigb.edu.cu> wrote: > Hi, > When I send the full log I received this mail from the list. > > - > > >

Re: [gmx-users] Problems with trjconv

On 2/16/18 2:35 PM, Poncho Arvayo Zatarain wrote: Hello Gomacs users: I have a problem with a lipid bilayer. The bilayers is inverted, the water is in the middle and the lipid tails are outside. How can i flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s file.tpr -n

[gmx-users] Problems with trjconv

Hello Gomacs users: I have a problem with a lipid bilayer. The bilayers is inverted, the water is in the middle and the lipid tails are outside. How can i flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s file.tpr -n index -o file.gro -pbc whole but nothing happens. In

Re: [gmx-users] GPU problem with running gromacs.2018

Hi, When I send the full log I received this mail from the list. - Your mail to 'gromacs.org_gmx-users' with the subject Re: [gmx-users] GPU problem with running gromacs.2018 Is being held until the list moderator can review it for approval. The reason it

Re: [gmx-users] GPU problem with running gromacs.2018

Hi, Indeed, this is an issue introduced in the 2018 release which aborts mdrun if an error is encountered during GPU detection; My first guess is that one of your GPUs is in exclusive or prohibited mode. You can use mdrun by skipping that GPU, i.e. setting the CUDA_VISIBLE_DEVICES environment

[gmx-users] GROMACS 2016.5 released

Hi GROMACS users, The official release of GROMACS 2016.5 is available! This release fixes several minor issues found since 2016.4. It incorporates all the fixes found in the 5.1.5 release. We encourage all users of the 2016 series to update to 2016.5. Please see the link to the release notes

Re: [gmx-users] GPU problem with running gromacs.2018

This is the output with gromacs 2018 and cuda 9 ---Program: gmx mdrun, version 2018Source file: src/gromacs/gpu_utils/gpu_utils.cu (line 735)Function:void findGpus(gmx_gpu_info_t*) Assertion failed:Condition: cudaSuccess ==

Re: [gmx-users] Flip a bilayer

On 2/15/18 12:38 PM, Poncho Arvayo Zatarain wrote: Hello Gromacs users: I have a problem with a lipid bilayer, when i watch in vmd, is inverted, the water is in the middle and the lipid tails are outside. How can i flip it to a correct way? I´m trying with gmx trjconv -f file.gro -s

Re: [gmx-users] Secondary structure propensity.

On 2/16/18 3:40 AM, Subhomoi Borkotoky wrote: Hello, I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file , it contains the required information. Only indirectly, but scount.xvg has all that is needed, the number of residues in a given secondary structure as a function of

[gmx-users] 2018 performance question

hi just installed gmx-2018 on a x86_64 PC with a Geforce GTX 780 and the cudasoftware directly from the nvidia webpage (didn't work using the debian nvidia packages) output of lscpu is included below. i find that: 1) 2018 is slightly faster (~5%) than 2016.2) both 2016 and 2018 use the GPU,

Re: [gmx-users] Secondary structure propensity.

Hello, I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file , it contains the required information. Regards, S. Borkotoky On Fri, Feb 16, 2018 at 1:30 PM, Sundari wrote: > Dear gromacs users, > > can any one please tell me that how we get the secondary

[gmx-users] (no subject)

Dear gromacs users, can any one please tell me that how we get the secondary structure propensity or secondary structure content(%) as a function of simulation time. I used "gmx do_dssp" but it gives me number of residues forming the secondary structure vs simulation time. is it same thing or

[gmx-users] Secondary structure propensity.

Dear gromacs users, can any one please tell me that how we get the secondary structure propensity or secondary structure content(%) as a function of simulation time. I used "gmx do_dssp" but it gives me number of residues forming the secondary structure vs simulation time. is it same thing or