[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

[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 referen

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

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 sim

[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 (contraint_rat

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 follow

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

[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 mad

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 e

[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 __

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

Hello, What I want to do is calculate the free energy difference of pulling the ligand away from the receptor. I want to do it using theromdynamic intergration using the Lamda 0/1 stuff. I am just not clear of the procedure of how to do it. I want to constraint several distances between the ligan

[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. I

[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 analysi

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 >

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 work

[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 did

[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 to

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 ac

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 a

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 >> m

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 sa

[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 r

[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