[gmx-users] Correcting for box jumps in pdo file

Dear all, I want to know if someone has had the same problem as me. I am running AFM calculations. when trying to plot the data from the pdo file, I can see that the coordinates are not fixed for jumps! The pulled group coordinates sometimes stay the same while the Reference and spring coordinate

Re: [gmx-users] Pbc and Com in simulation video

Hello Janne, this is what I usually do when my molecules cross the box or dance all around and it works for me: I first do this with the original unmodified or fitted xtc or trr file: trjconv -f -o -pbc nojump then i take the modified trr or xtc and do a fit: trjconv -f -s -fit rot+trans

[gmx-users] PMF from AFM pulling

Dear gromacs users, I would like to obtain a potential of mean force (PMF) plot from an AFM Pulling calculation. I used AFM method in the Pull code to separate two strands of peptides along their center of mass reaction coordinate. here is the parameters I used: runtype = afm ngroups = 1

Re: [gmx-users] Pull code methods?

Hi Maik, Thank you for the answer. I still have some questions. I still didn't get the umberalla sampling method. It seems to me AFM and umberalla are the same except that in umberalla we dont define a Pull rate. Looking at the literature, people have been using umberalla method with discrete

[gmx-users] Pull code methods?

Dear all, I have been reading the literature, mailing list and the manual. There is some questions that I cant understand: 1) there is three methods for the pull code: constraint force, AFM and umberalla. in both AFM and Constraint force, there is an option of the rate of pulling

Re: [gmx-users] Re: question about free energy. Gromacs user

Thank you David and Arneh for the comments. I just have a couple of things i want to clarify about the constrain distances i used. The distance I used to pull the ligand and receptor apart was a non-bonded distance between the amide nitrogen of the ligand and the oxygen carbonyl of the receptor

Re: [gmx-users] Constrains and TI

Thank you for the reply, Sorry for the confusion of my two emails. I guess I was using the word pulling in the wrong context. Now after my extensive reading, what I meant is that i want to calculate the absoulte binding free energy of a ligand/receptor complex. I have read the manual over and

Re: [gmx-users] Parellel Gromacs

Hello, I have tried using the mdrun_mpi and it can't run. It gives me this error: Failed to find the following executable: Executable: mdrun_mpi Cannot continue. Belquis I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename did you try the following

[gmx-users] Parellel Gromacs

Dear Gromacs users, I am trying to do Parellel calculations using Gromacs on a Rocks cluster that has MPI enabled. Has anybody encountered the following error: Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file RecpAntiP-cl#1-SG-consP-L0-1-G.tpr was

Re: [gmx-users] Parellel Gromacs

Hi, I am not the one who built it, but it is MPI supported. Have your built the GROMACS with MPI-support? Regards, Yang Ye On 8/1/2007 4:35 AM, [EMAIL PROTECTED] wrote: Dear Gromacs users, I am trying to do Parellel calculations using Gromacs on a Rocks cluster that has MPI

Re: [gmx-users] Error in pr

hi, did u specify an index file in your command line for the 2 groups (protein and SOl? Dhananjay, Consider searching the list archive... All possible solutions are in there. Cheers, Tsjerk On 7/27/07, Dhananjay [EMAIL PROTECTED] wrote: Hello all, I am getting error in pr

[gmx-users] Constrains and TI

hello all, is it possible to constrain a distance (or several) between a ligand-receptor complex inorder to simulate free energy change of separating the ligand from the receptor? I intend to use TI and lamda to do free energy calculations. any help is appreicated. Belquis

[gmx-users] free energy calculation and constraint distance?

Hello Gromacs users, I am trying to do a free energy calculation, which I have never done before. I have read the manual and the tutorial on the wiki but there is still some issues not clear to me. I am trying to calculate free energy difference of pulling the ligand from a beta-sheet receptor.

[gmx-users] representative structure using g-cluster

hello all, I am trying to get the best representative structure of a 40ns MD of a receptor to use for free energy calculations. I want to have an idea what is the best way to do that. I am using g_cluster with the gromos method. Is there a way to estimate the noise errors of the cluster

[gmx-users] trjconv -pbc?

Hello all, I have tried using trjconv -pbc(all options) to get a continuous trjactoary visulations on VMD. I am modeling an 11 residue receptor antiparellel to itself and one of the receptor strand jumps outside the box sometimes. I have used search to solve the problem but everthing i tried

Re: [gmx-users] trjconv -pbc?

Hi Tsjerk, Thank you for replying. I did give it a reference structure where the two parts are together. I solved the problem finally! I had a 10ns simulation before that and I used -pbc nojump on the original trjactory and it worked fine..but when I did it for the extra 10 ns i ran, it didnt

Re: [gmx-users] trjconv -pbc?

Hi TSjerk, Thanks for the explaination. It is appreciated. Belquis Hi Belquis, Just some background on the issue. The reason that your solution worked, and therefore the failure of your first procedure, is that in the second case the frame at t=10ns was modified using the frame at

[gmx-users] Trjconv: reducing frames and Time issue

Hello All, I have a xtc file and I used trjconv on it to reduce the number of frames using: trjconv -f original.xtc -o reduced-frames.xtc -s xx.tpr -timestep 20 -fit rot+trans -skip 2 -center no Now I have two xtc files for a 10ns simulation: original.xtc reduced-frames.xtc I did gmxcheck

[gmx-users] Restarting a crashed MD run

Hello all, I restarted a crashed run due to power outage using these command lines: tpbconv -s md0-30ns.tpr -f md0-30ns.trr -e md0-30ns.edr -o md0-30ns-C.tpr then mdrun -s md0-30ns-C.tpr -e md0-30ns-C.edr -o md0-30ns-C.trr -x md0-30ns-C.xtc -c after_md0-30ns-C.gro -g md0-30ns-C.log The

Re: [gmx-users] Restarting a crashed MD run

Hi Tsjerk, thank u for the answer. I checked my mdp file (nstvout=0). I just want to make sure that since nstvout=0 in my mdp file, and I used tpbconv means that it generated the run from the beginning of the crashed run? not the last frame? i Belquis Hi Belquis, I think you have the same

Re: [gmx-users] Restarting a crashed MD run

Hi, I ran gmxcheck and 0 frames have velocities. so it means it started from beginning? Belquis [EMAIL PROTECTED] wrote: Hi Tsjerk, thank u for the answer. I checked my mdp file (nstvout=0). I just want to make sure that since nstvout=0 in my mdp file, and I used tpbconv means that

Re: [gmx-users] Restarting a crashed MD run

sorry to ask again, I hope this is my last question about this. since I know now that the restarted run I did started from 0 time. I killed the job and it wrote velocity for the last frame. So since i knew i have to contiune this run that I just killed, I used tpbconj and it wrote a new tpr file

Re: [gmx-users] Restarting a crashed MD run

Thank you. I will save some energies and velocities in future simulations. but in this email, my job was not crashed..I terminated it and it wrote the last velocities and when i wanted to contiune it using pbdconj, it said it will finish the simulation from the time I terminated it. so is this

[gmx-users] use of -dt

Hi, I know this should be trivial..but i cant understand what this option do: -dtOnly write frame when t MOD dt = first time (ps) would some explain what is MOD and how this is relevent to g_cluster or trjconv. Thank u ___ gmx-users mailing list

[gmx-users] system goes out of the water box

Hello all, I am new to using Gromacs and MD simulation. I am simulating a 9-residue drug with a box of water. I generated the box using this: editconf -f xx.gro -o xx.gro -d 0.5 -bt cubic everything seems fine and the MD run went smooth. However when I look at the trajectory, I see that the drug