[gmx-users] Typo in table 3.1 of the reference manual?

Dear all, There is an inconsistency in the truncated octahedron entry in table 3.1 of the reference manual (version 2018 and all previous ones I checked). The value indicated for the bc and ab angles is 71.53 degrees, but the vectors a, b and c indicated in the table give the value 70.53

Re: [gmx-users] Domain Decomposition

Hi, You have a bonded interaction at a distance of 10 nm. I assume that's not your intention. Perhaps you should give a configuration to grompp that has whole molecules. IIRC less ancient versions of GROMACS do a better job of this. Mark On Thu, Feb 15, 2018 at 5:39 PM Iman Ahmadabadi

Re: [gmx-users] gmx insert-molecule issue- not getting the number atoms inserted wanted

Hi, There's not enough information to say. What makes you think your molecules will fit in the spaces you say are there? What radii did you suggest for the atoms in your molecules? Mark On Thu, Feb 15, 2018 at 6:54 PM Joydeep Munshi wrote: > Hello, > > I have a system of

Re: [gmx-users] compiling 2018 with GPU doesn't work on my debian stretch

Szilárd wrote:> Option A) Get a gcc 5.x (e.g. compile from source) > Option B) Install CUDA 9.1 (and required driver) which is compatible > with gcc 6.3 > (http://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html) didn't try A (there might be a good reason why stretch does not have

[gmx-users] gmx insert-molecule issue- not getting the number atoms inserted wanted

Hello, I have a system of polymer(P3HT)-fullerene system. I am using initially Insert-molecule command to insert N number of P3HT molecules followed by PCBM molecules. Finally I am solvating the system using Solvate command. While I am trying to insert N=300 atoms it is successfully inserting

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

Yes, it is true, sorry, but I have problems with both. With version 2018 the error it's diferent. that's why i compiled an older version. Osmany -Original Message- From: Szilárd Páll Reply-to: gmx-us...@gromacs.org To: Discussion list for GROMACS users

[gmx-users] Flip a bilayer

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 file.tpr -n index -o file.gro -pbc whole but nothing happens.

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

PS: Also, what you pasted in here states "2016.4", but your subject claims version 2018 -- Szilárd On Thu, Feb 15, 2018 at 6:23 PM, Szilárd Páll wrote: > Please provide a full log file output. > -- > Szilárd > > > On Thu, Feb 15, 2018 at 6:11 PM, Osmany Guirola Cruz >

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

Please provide a full log file output. -- Szilárd On Thu, Feb 15, 2018 at 6:11 PM, Osmany Guirola Cruz wrote: > Hi > > I am having problems running mdrun command compiled with GPU > support(cuda 9.0). > here is the output of the mdrun command > >

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

Hi I am having problems running mdrun command compiled with GPU support(cuda 9.0). here is the output of the mdrun command Using 1 MPI thread Using 4 OpenMP threads 1 compatible GPU is present, with ID 0 1 GPU auto-selected for this run. Mapping of GPU ID to the 1 PP rank in

[gmx-users] Domain Decomposition

Dear Gromacs Users, In one job, I always get in (any number of nodes) the domain decomposition error as following and I don't know what should I do. I have to use the -dds or -rdd setting for my problem? Sincerely Iman Initializing Domain Decomposition on 56 nodes Dynamic load balancing: auto

[gmx-users] further compilation issues on stretch

as compilation of gmx-2018 idn't work for me i went back to 2016.4 after some google-ing i found that the following commands work, and gmx compiles without any complaints... > cmake .. -DGMX_GPU=on  -DNVML_FOUND=1 > -DNVML_LIBRARY=/usr/lib/x86_64-linux-gnu/libnvidia-ml.so.1 >

Re: [gmx-users] using enegygrps

Hi Dr.Lemkul Thank you very much for your answer, it was very great help for me Thank you Regards Azadeh -- This email was Anti Virus checked by Security Gateway. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] compiling 2018 with GPU doesn't work on my debian stretch

Option A) Get a gcc 5.x (e.g. compile from source) Option B) Install CUDA 9.1 (and required driver) which is compatible with gcc 6.3 (http://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html) -- Szilárd On Thu, Feb 15, 2018 at 2:34 PM, Michael Brunsteiner wrote: >

[gmx-users] compiling 2018 with GPU doesn't work on my debian stretch

Hi, I have problems compiling gromacs-2018 (January 10 release) on debian stretch (vanilla) my specs: Linux 4.9.0-4-amd64 #1 SMP Debian 4.9.65-3+deb9u1 (2017-12-23) x86_64 GNU/Linux gcc-6.3.0,Cuda compilation tools, release 8.0, V8.0.44 graphics: Geforce GTX 780. I do: > cmake .. -DGMX_GPU=on

Re: [gmx-users] Rupture force definition

On 2/15/18 4:13 AM, Rakesh Mishra wrote: Dear Justin thanks for your advise. I will check for longer run for getting response according to you. I would like to explain my system,which is siRNA of chain A and B. Here, after doing all formalities, I had run 10 ns then try to apply the pull

Re: [gmx-users] using enegygrps

On 2/15/18 4:17 AM, kordza...@aut.ac.ir wrote: Hi Dr.Lemkul you said, the breaking molecule occured because of period boudary condition, isnt it a problem? because before your answer I thought I must select bigger box in order to the breaking wont occur. but now I understand the beaking

Re: [gmx-users] using enegygrps

On 2/14/18 11:16 PM, kordza...@aut.ac.ir wrote: Hi Dr.Lemkul Thank you very much for your answer and your time I m using Gromos 54a7 force field, How can I find my force field is parametrized in such a way that the nonbonded energy decomposition has some physical meaning? In your case,

Re: [gmx-users] Potential issue using acpype to convert amber topology to gromacs

Hi Justin, That makes sense, I've found where the parameters are Thanks for your help James From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: 14

Re: [gmx-users] using enegygrps

Hi Dr.Lemkul you said, the breaking molecule occured because of period boudary condition, isnt it a problem? because before your answer I thought I must select bigger box in order to the breaking wont occur. but now I understand the beaking isnt a problem. I have another question, what is

Re: [gmx-users] Rupture force definition

Dear Justin thanks for your advise. I will check for longer run for getting response according to you. I would like to explain my system,which is siRNA of chain A and B. Here, after doing all formalities, I had run 10 ns then try to apply the pull protocol. See, here for pulling this system, I

Re: [gmx-users] Flexible and posres

Dear Justin and Mark, The define = -DPOSRES -DFLEXIBLE is correct and thank you so much for your help. Respectfully, Iman On Wed, Feb 14, 2018 at 11:17 PM, Iman Ahmadabadi < imanahmadabad...@gmail.com> wrote: > Dear Justin, > > Because there is a movement on atoms that posres should act on