Re: [gmx-users] DSSP with custom residues

but it is not working and I got confused! I have 10 residues and 400 ns time simulations ( 80001 frames). For this file how can I fix the xbox and ybox parameters? Thanks in advance, On Tue, Apr 26, 2016 at 3:12 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/26/16 9:10 AM, lei

Re: [gmx-users] DSSP with custom residues

Hi Justin, I am also busy by DSSP analysis. I am interested to know what the difference between do_dssp and dssp is? Regards, Leila On Tue, Apr 26, 2016 at 3:00 PM, Justin Lemkul wrote: > > > On 4/26/16 8:57 AM, Stephanie Jephthah wrote: > >> Hi! >> >> I'm simulating a

[gmx-users] g_helix

Dear all, I have a question regarding to calculate g_helix, I am not sure about the index numbers for using g_helix! Should I use the all atom numbers of protein that I have? If not please explain to me which indexes of protein I have to choose. The same for do_dssp, I have to use the all atom

Re: [gmx-users] save the trajectory

the > distance between the surface and the polymer as a function of the time. > Then you can use trjconv with the b and e flags to get that part of the > trajectory. > > Kind regards > > Dries > On 4 Mar 2016 4:11 p.m., "leila salimi" <leilasal...@gmail.com> wro

Re: [gmx-users] problem to restart REMD

Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of leila salimi leilasal...@gmail.com Sent: Friday, June 26, 2015 1:30 PM

Re: [gmx-users] problem to restart REMD

appending, that's just for convenience. The advice about node count mismatch doesn't matter here... Use your judgement! Mark On Thu, 25 Jun 2015 16:23 leila salimi leilasal...@gmail.com wrote: Thanks very much. Ok I will check again, it seems that they are at the same step! only

Re: [gmx-users] problem to restart REMD

Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of leila salimi leilasal...@gmail.com Sent: Friday, June 26, 2015 1:30 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users

Re: [gmx-users] problem to restart REMD

but buffer size is 32 ERROR: 0031-300 Forcing all remote tasks to exit due to exit code 1 in task 896 job.err.1011016.out 399L, 17608C Actually I don't know what is the problem! Regards, Leila On Thu, Jun 18, 2015 at 12:00 AM, leila salimi leilasal...@gmail.com wrote: I understand what you meant

Re: [gmx-users] problem to restart REMD

PM leila salimi leilasal...@gmail.com wrote: Dear Mark, When I tried with new update of the state.cpt files, I got this error. Abort(1) on node 896 (rank 896 in comm 1140850688): Fatal error in MPI_Allreduce: Message truncated, error stack: MPI_Allreduce(912)...: MPI_Allreduce

Re: [gmx-users] problem to restart REMD

Hi Mark, Thanks very much. Unfortunately both the state6.cpt, state6_prev,cpt and state7.cpt and state7_prev.cpt updated and their time are different from other replicas file (also with *_prev.cpt )! I am thinking maybe I can use init-step in mdp file, and start from the time that I have,

Re: [gmx-users] problem to restart REMD

I understand what you meant, I run only few steps for the other replicas and then continue with the whole replicas. I hope every thing is going well. Thanks very much. On Wed, Jun 17, 2015 at 11:43 PM, leila salimi leilasal...@gmail.com wrote: Thanks Mark for your suggestion. Actually I don't

Re: [gmx-users] problem to restart REMD

, 2015 at 10:18 PM leila salimi leilasal...@gmail.com wrote: Hi Mark, Thanks very much. Unfortunately both the state6.cpt, state6_prev,cpt and state7.cpt and state7_prev.cpt updated and their time are different from other replicas file (also with *_prev.cpt )! I am thinking maybe I

[gmx-users] PMF calculation with constraint distance

Hi all, I started to calculate PMF between two ions in solution and I used constraint for pull option, instead of umbrella as I saw in Umbrella sampling Tutorial of Justin. This is the part of my mdp file! ; Pull code pull= constraint; Justin's value was umbrella pull_geometry

Re: [gmx-users] PMF calculation with constraint distance

for each constrained distances around 15 ps MD and then I used averaged forces for each distances! Cheers, Leila On Thu, May 21, 2015 at 11:04 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/21/15 5:00 PM, leila salimi wrote: Hi all, I started to calculate PMF between two ions in solution

[gmx-users] RMSD between two groups

Dear all, I have a question regarding to analyse the trajectory that I have. I am studying the interaction of peptide at interfaces, e.g Oxygen of carboxylate group of side chains with Cations at the interface! I would like to calculate the distance between Oxygen of carboxylate group of side

Re: [gmx-users] g_rdf

? When we have two groups of atoms, the cumulative number is the average number of coordination between two groups of atoms? Regards, Leila On Mon, Feb 23, 2015 at 1:39 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/23/15 6:50 AM, leila salimi wrote: Dear all, I have a question regarding

[gmx-users] g_rdf

Dear all, I have a question regarding radial distribution function. Does g_rdf program work for non-cubic cell eg. triclinic? Regards, Leila -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] Error on restart REMD simulations

Dear Gromacs users, When I tried to restart my REMD simulations, I got this error : Fatal error: The 16 subsystems are not compatible When I checked the cpt files I found that 2 replicas have different time from other replicas, and I knew that the error comes from this issue. For example

[gmx-users] odd replica excahnge

Dear gromacs users, I have tried different replica exchanges for my system, like 12, 14. I found that with 15 replica, I can get 30-40 % ratio of exchanges between replicas! When I sumbitted a simulation with 15 replicas, I did not get any result and I got this error : ERROR: 0031-725 Failed to

Re: [gmx-users] odd replica excahnge

wrote: On Mon, Dec 1, 2014 at 4:39 PM, leila salimi leilasal...@gmail.com wrote: Dear gromacs users, I have tried different replica exchanges for my system, like 12, 14. I found that with 15 replica, I can get 30-40 % ratio of exchanges between replicas! I don't understand. Below

[gmx-users] size of the box for peptide

Dear gromacs users, I want to simulate the conformation of peptide in solution (20 monomers of Glutamate with solution). I am in doubt about the size of the box, and number of water molecules. I want to consider rhombic dodecahedron box. For example I chose a box with approximately 498 nm^3 that

[gmx-users] does not appear to contain CMakeLists.txt Error to compile GROMACS 4.6.3

Dear GROMACS Users, I tried to compile GROMACS on my computer, I did a quick installation as I saw in the link tar -xvzf gromacs-4.6.1.tar.gz $ cd gromacs-4.6.1 $ mkdir build $ cd build ( I did not have cmake and I got it form sudo apt-get install cmake in build folder, then I tried the

Re: [gmx-users] does not appear to contain CMakeLists.txt Error to compile GROMACS 4.6.3

On Tue, Jul 22, 2014 at 6:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/22/14, 12:25 PM, leila salimi wrote: Dear GROMACS Users, I tried to compile GROMACS on my computer, I did a quick installation as I saw in the link tar -xvzf gromacs-4.6.1.tar.gz $ cd gromacs-4.6.1 $ mkdir

Re: [gmx-users] does not appear to contain CMakeLists.txt Error to compile GROMACS 4.6.3

What does this sentence mean? Run CMake with the path to the source as an argument On Tue, Jul 22, 2014 at 7:00 PM, leila salimi leilasal...@gmail.com wrote: On Tue, Jul 22, 2014 at 6:46 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/22/14, 12:25 PM, leila salimi wrote: Dear GROMACS

Re: [gmx-users] does not appear to contain CMakeLists.txt Error to compile GROMACS 4.6.3

Thanks, I tried with 4.6.6 , the same as I did before for 4.6.3 and It works now (4.6.6) ! On Tue, Jul 22, 2014 at 9:33 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/22/14, 1:19 PM, leila salimi wrote: What does this sentence mean? Run CMake with the path to the source as an argument

[gmx-users] Group vs Verlet pair-lists

Dear GROMACS Users, I have a question regarding the Neighbor searching, I used group scheme when I used 4.5 and now I found that there is verlet in version 4.6. When I compare the trajectories, For verlet simulation I found that the atoms of water molecules are separated and it caused the long

[gmx-users] Group vs Verlet pair-lists

Dear GROMACS Users, I have a question regarding the Neighbor searching, I used group scheme when I used 4.5 and now I found that there is verlet in version 4.6. When I compare the trajectories, For verlet simulation I found that the atoms of water molecules are separated and it caused the long

Re: [gmx-users] cutoff-sch​eme in CPU GPU

Dear GROMACS Users, I have a question regarding the Neighbor searching, I used group scheme when I used 4.5 and now I found that there is verlet in version 4.6. When I compare the trajectories, For verlet simulation I found that the atoms of water molecules are separated and it caused the long

Re: [gmx-users] Group vs Verlet pair-lists

Thanks Justin. On Wed, Jul 16, 2014 at 8:42 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/14, 2:21 PM, leila salimi wrote: Dear GROMACS Users, I have a question regarding the Neighbor searching, I used group scheme when I used 4.5 and now I found that there is verlet in version 4.6

[gmx-users] partial charge and LJ parameters for CH3 in gromos forcefields

Dear users, I have CH3 in my molecule and in gromos force filed partial charges for CH3 is 0 (as the united atom of the GROMOS forcefield) and It doesn't consider single H atoms, but includes these H atoms into the C atoms. That means that the CH3 group is just one LJ-bead in the GROMOS

[gmx-users] Type of function for bond or bend in SPC/E or TIP3P model

Dear All, I would like to be sure about the formula for Bond and Angle in itp files, like for SPC/E or TIP3P? Is it like a harmonic form 1/2*K*(R-R0)^2 or K*(R-R0)^2 ? Thanks very much and regards, Leila -- Gromacs Users mailing list * Please search the archive at