Re: [gmx-users] PCA and FEL

Hi Suniba, No, with gmx anaeig you can select -2d, which does a 2D projection onto the selected eigenvectors. Alternatively, you can combine any two projections onto eigenvectors, which you get using the option -proj. The quickest way to do that is something like: paste <(grep -v '^[@#]'

[gmx-users] PCA and FEL

Hello everyone I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis for the stability of my pro-lig complex. In a 2015 paper, The group calculated two principal component, PC1 and PC2 and then prepared an.xvg file to be used as input for g_sham. My question is, when we use

[gmx-users] Umbrella Sampling - choice of pull-coord?-dim

Dear GROMACS users, I am interested in the role of the mdp parameter pull-coord?-dim when sampling a particular umbrella window after having generated initial configurations for, say, the COM distance between two groups being the reaction coordinate. I know that these options can be controlled

Re: [gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

On 5/14/16 2:34 PM, Mark Abraham wrote: Hi, Please keep the discussion on the mailing list, so others can help and learn. Antara said: I have pasted the mdrun command i used to run it in parallel with the number of processors i used which was 16. The command is :

[gmx-users] COM-Pull along a direction

Dear Gromacs users, I am trying to pull an ion out of a protein using Gromacs/5.0.4. I pull the ion along specific pre-determined paths. From my understanding, pulling along a direction _V guarantees that the dumb bead would move only at direction _V. The position of the dumb bead is

Re: [gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

Hi, Please keep the discussion on the mailing list, so others can help and learn. > Antara said: > I have pasted the mdrun command i used to run it in parallel with the number of processors i used which was 16. The command is : > > >/app/setups/gromacs-5.1.1/build/bin -deffnm MD -pin on -rdd 1.8

Re: [gmx-users] (no subject)

I would use -dump to extract only the last frame, I believe that what your are doing is saving your trajectory in a pdb file. On 14 May 2016 at 16:21, Mark Abraham wrote: > Hi, > > Sure, but if you have a million frames, then you are probably doing > something other

Re: [gmx-users] (no subject)

Hi, Sure, but if you have a million frames, then you are probably doing something other than what you want or should do. See http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume Mark On Sat, May 14, 2016 at 5:15 PM Upasana Ray wrote: > I

Re: [gmx-users] (no subject)

I have modelled my protein using homology modeling software & then have used gromacs for energy minimization. gmx trjconv -f md22.xtc -s md22.tpr -o md22.pdb then I have choosen only protein from the options On Sat, May 14, 2016 at 3:55 PM, Pratiti Bhadra wrote: > How

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Hi, On Sat, May 14, 2016 at 1:09 PM wrote: > In case it's relevant/interesting to anyone, here are the details on our > cluster nodes: > > nodes # model # cores cpu model > RAM node_type > fmb01 - fmb33 33

Re: [gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

Hi, On Sat, May 14, 2016 at 4:34 PM Antara mazumdar wrote: > Dear users, > > I am trying to run a coarse grained simulation of a membrane protein in a > mixed lipid billayer using martini model 2.2. I have already performed all > the equilibration steps successfully on

[gmx-users] error in running mdrun of membrane protein in a mixed bilayer with MARTINI MODEL

Dear users, I am trying to run a coarse grained simulation of a membrane protein in a mixed lipid billayer using martini model 2.2. I have already performed all the equilibration steps successfully on my desktop with GROMACS 5.1.0. However, when i try to execute its production run in

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

In case it's relevant/interesting to anyone, here are the details on our cluster nodes: nodes # model # cores cpu model RAM node_type fmb01 - fmb33 33 IBM HS21XM 8 3 GHz Xeon E5450

Re: [gmx-users] (no subject)

How many frames do u save using trjconv?. Can you please post your full trjconv command here. On 14 May 2016 18:21, "Chalaoux, Francois-Regis" < francois-regis.chala...@evotec.com> wrote: > What is your protein, PDB Id ? > > FR. > > > Le 14 mai 2016 à 12:04:09, Upasana Ray

Re: [gmx-users] (no subject)

What is your protein, PDB Id ? FR. > Le 14 mai 2016 à 12:04:09, Upasana Ray a écrit : > > yes I have removed water & the pdb file only contains protein > > On Sat, May 14, 2016 at 1:50 PM, Chalaoux, Francois-Regis < > francois-regis.chala...@evotec.com> wrote: > >>

Re: [gmx-users] (no subject)

yes I have removed water & the pdb file only contains protein On Sat, May 14, 2016 at 1:50 PM, Chalaoux, Francois-Regis < francois-regis.chala...@evotec.com> wrote: > Hi, > > Did you removed Water ? > Check also there is no other protein in the same file. > > FR. > > > Le 14 mai 2016 à

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

On 5/14/16 3:48 AM, Husen R wrote: Hi, Currently I'm running this tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html) to simulate restart with fewer nodes. at restart, I changed the amount of nodes from 3 to 2 nodes. I also changed the amount

Re: [gmx-users] simulation_time

On 5/14/16 2:25 AM, Ms. Nikita Bora wrote: Respected Sir, Recently i followed your tutorial for simulation of a 50 ns final mdrun of protein-ligand complex where the value of rvdw=rcoulomb=1.4 was used. The simulation runned at aorund 10 ns/day . While for the same complex when

Re: [gmx-users] (no subject)

Hi, Did you removed Water ? Check also there is no other protein in the same file. FR. > Le 14 mai 2016 à 07:04:15, Upasana Ray a écrit : > > Dear user, > > I have generated my final protein.pdb file by using trjconv command from > .xtc file. The size of my pdb

Re: [gmx-users] Restart simulation from checkpoint file with fewer nodes

Hi, Currently I'm running this tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/08_MD.html) to simulate restart with fewer nodes. at restart, I changed the amount of nodes from 3 to 2 nodes. I also changed the amount of processes from 24 to 16 processes.

[gmx-users] simulation_time

Respected Sir, Recently i followed your tutorial for simulation of a 50 ns final mdrun of protein-ligand complex where the value of rvdw=rcoulomb=1.4 was used. The simulation runned at aorund 10 ns/day . While for the same complex when rvdw=rcoulomb=1 is made the run was 10 ns/day. Sir i would

Re: [gmx-users] (no subject)

Hi Upasana, What is your goal, your research objective? 'opening it for docking purpose' is way too vague for us to help you, other then suggesting that you are probably not choosing an optimal approach. Cheers, Tsjerk On May 14, 2016 07:04, "Upasana Ray" wrote: >