[gmx-users] System Blowing up when more than one MPI thread is used

2019-03-22 Thread Mayank Vats
Hi, I am trying to do a simple simulation in GROMCAS 2018.6, of a protein in tip3p water with the amber99 forcefield. Its a 14nm cubic box with two protein chains, and 87651 water molecules, 269525 atoms total. I am able to energy minimise to an Fmax < 500, and then perform nvt and npt equilibriati

Re: [gmx-users] system blowing up

2016-12-02 Thread Justin Lemkul
On 12/1/16 1:23 PM, abhisek Mondal wrote: Hi, I'm constantly getting a strange error of system blow up during equilibration procedure. I'm relatively new to gromacs, please help me to get my things straight. I have a ligand bound protein structure in solvated condition. So, I was using: gmx m

[gmx-users] system blowing up

2016-12-01 Thread abhisek Mondal
Hi, I'm constantly getting a strange error of system blow up during equilibration procedure. I'm relatively new to gromacs, please help me to get my things straight. I have a ligand bound protein structure in solvated condition. So, I was using: gmx mdrun -v -deffnm em #for minimization Upon suc

Re: [gmx-users] System blowing up in final MD run

2016-07-13 Thread Deep Bhattacharya
Thank you Justin. Sent from my iPhone > On Jul 13, 2016, at 8:13 AM, Justin Lemkul wrote: > > > >> On 7/13/16 9:12 AM, Deep Bhattacharya wrote: >> Sure. I will use the PME henceforth. Are the other parameters okay in the >> .mdp file? > > I made several comments, embedded within the .mdp te

Re: [gmx-users] System blowing up in final MD run

2016-07-13 Thread Justin Lemkul
On 7/13/16 9:12 AM, Deep Bhattacharya wrote: Sure. I will use the PME henceforth. Are the other parameters okay in the .mdp file? I made several comments, embedded within the .mdp text. Correct all of them carefully. -Justin Sent from my iPhone On Jul 13, 2016, at 8:09 AM, Justin

Re: [gmx-users] System blowing up in final MD run

2016-07-13 Thread Deep Bhattacharya
Sure. I will use the PME henceforth. Are the other parameters okay in the .mdp file? Sent from my iPhone > On Jul 13, 2016, at 8:09 AM, Justin Lemkul wrote: > > > >> On 7/13/16 9:07 AM, Deep Bhattacharya wrote: >> Hello Justin, >> Is it appropriate to use Nose-Hoover thermostat with Parrin

Re: [gmx-users] System blowing up in final MD run

2016-07-13 Thread Justin Lemkul
On 7/13/16 9:07 AM, Deep Bhattacharya wrote: Hello Justin, Is it appropriate to use Nose-Hoover thermostat with Parrinello rahman thermostat in the .mdp file? In the previous mail I have reduced the time step , will all there changes be appropriate for the simulation ? It's fine as long as

Re: [gmx-users] System blowing up in final MD run

2016-07-13 Thread Deep Bhattacharya
Hello Justin, Is it appropriate to use Nose-Hoover thermostat with Parrinello rahman thermostat in the .mdp file? In the previous mail I have reduced the time step , will all there changes be appropriate for the simulation ? Sincerely, Deep Sent from my iPhone > On Jul 13, 2016, at 8:01 AM, Jus

Re: [gmx-users] System blowing up in final MD run

2016-07-13 Thread Deep Bhattacharya
Sent from my iPhone > On Jul 13, 2016, at 8:01 AM, Justin Lemkul wrote: > > > >> On 7/13/16 8:56 AM, Deep Bhattacharya wrote: >> Hello Tsjerk, >> >> These are the notes that I got before running the NPT equilibration >> >> >> NOTE 1 [file npt.mdp]: >> leapfrog does not yet support Nose-H

Re: [gmx-users] System blowing up in final MD run

2016-07-13 Thread Justin Lemkul
On 7/13/16 8:56 AM, Deep Bhattacharya wrote: Hello Tsjerk, These are the notes that I got before running the NPT equilibration NOTE 1 [file npt.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 165 of the 1596 non-bonded parameter combinations Excl

Re: [gmx-users] System blowing up in final MD run

2016-07-13 Thread Deep Bhattacharya
Hello Tsjerk, These are the notes that I got before running the NPT equilibration NOTE 1 [file npt.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Generated 165 of the 1596 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_

Re: [gmx-users] System blowing up in final MD run

2016-07-13 Thread Tsjerk Wassenaar
Hi Deep, What force field? What system? How many cores? Did you try running on one? What error? Did pdb2gmx or grompp give any warnings? Cheers, Tsjerk On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya wrote: > Hello, > My system is blowing up for the protein carbohydrate solvent complex. I

[gmx-users] System blowing up in final MD run

2016-07-12 Thread Deep Bhattacharya
Hello, My system is blowing up for the protein carbohydrate solvent complex. I have attached the mdp file below. The NPT and NVT were in good accordance to tutorial listed by Justin. 'Please help me solve the issue. title = CD44 complex MD simulation ; Run parameters integrator = md

Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

2015-12-16 Thread Justin Lemkul
On 12/16/15 12:54 PM, NISHA Prakash wrote: Dear Justin, You are right and I totally agree with you. But, the point that I was trying to make was that "the same input coordinates and input .mdp files run in 4.5.4 and fail in 5.0.5". Also, if this situation persists, does that mean the results

Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

2015-12-16 Thread NISHA Prakash
Dear Justin, You are right and I totally agree with you. But, the point that I was trying to make was that "the same input coordinates and input .mdp files run in 4.5.4 and fail in 5.0.5". Also, if this situation persists, does that mean the results that have been obtained from the version 4.5.4

Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

2015-12-16 Thread Justin Lemkul
On 12/16/15 12:08 AM, NISHA Prakash wrote: Dear Justin, I am simulating a protein ligand complex. The protein co-ordinate file that I have taken is an output of the simulation of the protein alone in Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still facing this problem whe

Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

2015-12-15 Thread NISHA Prakash
Dear Justin, I am simulating a protein ligand complex. The protein co-ordinate file that I have taken is an output of the simulation of the protein alone in Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still facing this problem wherein I get the LINCS warning for only the prote

Re: [gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

2015-12-15 Thread Justin Lemkul
On 12/15/15 8:42 AM, NISHA Prakash wrote: Hi all, I am trying to simulate a protein using similar parameters as in the tutorial - Protein ligand by Justin Lemkul. I am facing a problem wherein the protein simulation is exploding only in this version - Gromacs-v5.0.5 but not in the older versi

[gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

2015-12-15 Thread NISHA Prakash
Hi all, I am trying to simulate a protein using similar parameters as in the tutorial - Protein ligand by Justin Lemkul. I am facing a problem wherein the protein simulation is exploding only in this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4. The warning message is as

Re: [gmx-users] System blowing up at restart

2015-12-02 Thread Mark Abraham
Hi, That's indeed curious. Please open an issue at http://redmine.gromacs.org and attach your .tpr and .cpt files so we can see if we can reproduce it. Mark On Wed, Dec 2, 2015 at 9:22 PM Marlon Sidore wrote: > It actually went on a few steps before blowing up, it didn't blow up > directly at

Re: [gmx-users] System blowing up at restart

2015-12-02 Thread Marlon Sidore
It actually went on a few steps before blowing up, it didn't blow up directly at restart. Does that mean it simply blew up because of the system ? It always blows up a little time after restarting though, and that's strange given the time it ran the first time. gmx dump doesn't say anything specia

Re: [gmx-users] System blowing up at restart

2015-12-02 Thread Mark Abraham
Hi, That should work, and I can't see why it should ever blow up. What does gmx dump have to say about vict.cpt? Does the restarted .log file say after the restart? Mark On Wed, Dec 2, 2015 at 8:20 PM Marlon wrote: > Hello, > > I have a problem continuing my simulation after the queue system s

[gmx-users] System blowing up at restart

2015-12-02 Thread Marlon
Hello, I have a problem continuing my simulation after the queue system stops the job (as I can't get -maxh to work). I would like to append the files to the old ones. The first production run, which ran one full day and 155 million steps, had the mdrun options: mdrun_mpi -deffnm vict -cpi equil.

Re: [gmx-users] System blowing up - equilibration step - CG simulation

2015-03-06 Thread Tsjerk Wassenaar
Hi Carlos, You can try to contact Floris about the MGDG model. Cheers, Tsjerk On Fri, Mar 6, 2015 at 9:56 PM, Carlos Navarro Retamal wrote: > Hi Tsjerk, > I tried to follow as closer as i could the parameters you used, but again > without luck: > .mdp file: > dt = 0.01 > nsteps

Re: [gmx-users] System blowing up - equilibration step - CG simulation

2015-03-06 Thread Carlos Navarro Retamal
Hi Tsjerk, I tried to follow as closer as i could the parameters you used, but again without luck: .mdp file: dt = 0.01 nsteps = 500 nstxout = 0 nstvout = 0 nstlog = 1 nstxtcout= 1000 xtc-precision= 10 rlist

Re: [gmx-users] System blowing up - equilibration step - CG simulation

2015-03-06 Thread Tsjerk Wassenaar
Hi Carlos, Most of that work (and the tutorials) was started some time ago. You can use Gromacs 5. At some point, the tutorials will get updated, but usually if there's pressure from a course or workshop. Otherwise the science comes first :) Cheers, Tsjerk On Mar 6, 2015 8:38 PM, "Carlos Navarro

Re: [gmx-users] System blowing up - equilibration step - CG simulation

2015-03-06 Thread Carlos Navarro Retamal
Hi Tsjerk, Thanks for your kind reply. I just start to reading your manuscript and notice that you used GROMACS version 4.5.5 instead of the latest one (5.X) Is there an specific reason to do these? (maybe martini works in a better way with older version of gromacs? ) I’m asking you these, becaus

Re: [gmx-users] System blowing up - equilibration step - CG simulation

2015-03-06 Thread Tsjerk Wassenaar
Hi Carlos, Other things to consider are doing a first short equilibration on a single processor and increasing the dom.dec. radius to 1.6 or 1.8 (mdrun -rdd 1.6). Maybe you might want to check the just accepted manuscript on thylakoid membranes from the Martini group ( http://dx.doi.org/10.1016/j.

Re: [gmx-users] System blowing up - equilibration step - CG simulation

2015-03-06 Thread Carlos Navarro Retamal
Dear Justin, I was looking into the paper where the ‘martini’ group described the parameters for glycolipids, and the mention that in order to equilibrate some glycolipids the had to used a timestep of 5fs. Sadly they not mention which glycolipid were, so i reduced the timestep from 20fs to 10fs

Re: [gmx-users] System blowing up - equilibration step - CG simulation

2015-03-06 Thread Carlos Navarro Retamal
Dear Justin, Thanks for your kind reply. Is there a way to set up a bilayer membrane system without a protein using insane? I’ve already several CG simulations with this protein, so i'm pretty sure that its parameters are ok. I do have some issues with the glycolipid used (MGDG) This is the firs

Re: [gmx-users] System blowing up - equilibration step - CG simulation

2015-03-06 Thread Justin Lemkul
On 3/6/15 8:15 AM, Carlos Navarro Retamal wrote: Dear Gromacs users, I'm trying to perform a CG simulations of a system consisting in a protein locate at 5 nm with respect to the charged groups of a MGDG membrane. I first performed an EM in vaccum. After that, to constructed the system i use i

[gmx-users] System blowing up - equilibration step - CG simulation

2015-03-06 Thread Carlos Navarro Retamal
Dear Gromacs users, I'm trying to perform a CG simulations of a system consisting in a protein locate at 5 nm with respect to the charged groups of a MGDG membrane. I first performed an EM in vaccum. After that, to constructed the system i use insane.py as following: ./insane.py -f minimization-va