[gmx-users] installing error

Hi there, I'm installing gromacs with these series of commands, sudo apt-get update sudo apt-get upgrade sudo apt-get install cmake cmake --version sudo apt-get install build-essential pwd cd Downloads/ wget http://gerrit.gromacs.org/download/regressiontests-5.1.1.tar.gz tar xvzf regressio

[gmx-users] Protein protein complex md simulaton

Dear all, Does there exist any differences between the steps to follow for protein and protein-protein complex md simulation? -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posti

[gmx-users] Multiple runs for same system

Hi, Can anyone tell me the steps and commands for performing multiple runs of 50 ns for same protein-ligand system? Also the clustering for further analyses. Thanks.  -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] Protein protein complex molecular dynamic simulation

Can molecular dynamic simulation be performed over protein-protein complexes using gromacs? Thanking you, -- Best regards, *Shyantani Maiti* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? R

Re: [gmx-users] installing error

Hi, Try getting a more up to date version from http://manual.gromacs.org/documentation/ and follow the quick installation guide there. Mark On Sat, Feb 24, 2018, 10:25 banijamali_fs wrote: > Hi there, I'm installing gromacs with these series of commands, > > sudo apt-get update > > sudo apt-ge

[gmx-users] tpr generation aborted

Hi, Following the Lusozume tutorial, I face an error at the step of generating ions.tpr which says too many warnings. $ gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr NOTE 1 [file ions.mdp]:   With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note   that with the

Re: [gmx-users] Why the '5-Helix' randomly displayed in the scount.xvg after running do_dssp?

Dear Cheng, Gromacs is open source. Implement this at your own will. If there is a sufficient interest in such a feature it might even have a place in the official release at some point. Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Curie

Re: [gmx-users] Potential energy coming out to be zero but not negative

Dear Shayantani, The output you quote show a negative potential energy. Is that not for the run you refer to? (With regards to “Hello Sir”, may I suggest a more gender inclusive greeting.) Kind regards, Erik __ Erik Marklund, PhD, Marie Skłodowska Cur

Re: [gmx-users] problems with the output of pullx

Hi, Updating my post. The problem has been observed in two different machine systems (the latest I have found the problem was the skylake nodes in tacc). I assumed it has to be some communication bug of coordinates and forces in the pull part of the code. Probably observed in my case because o

Re: [gmx-users] problems with the output of pullx

Hi, My (thoroughly uneducated) guess is that the spikes are related to the pull distance approaching half of the dimensions of the cell. Not all flavours of pulling can handle this. Might that be the issue? Mark On Sat, Feb 24, 2018, 17:55 alfredo wrote: > Hi, > Updating my post. The problem

Re: [gmx-users] problems with the output of pullx

Hi Mark, Thanks for your comment. No, that is not the problem. At that location the center of mass of the peptide is deep inside the membrane, separation between the two pulling groups is 0.4 nm and the dimension of the cell along z is more than 10 nm. I am only pulling along the z direction.