[gmx-users] Not able to continue with Equilibration

2012-03-29 Thread Hendry
Hi, I am using Gromacs 4.5.4. After successful minimization by SD, I continued with equilibration step but I got the below errors. I tried many times with different parameters but the problem still persists. I have given errors and md parameters of equilibration step below. I have also provided

[gmx-users] Not able to continue with Equilibration

2012-03-29 Thread chris . neale
liche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von francesca vitalini Gesendet: Donnerstag, 29. März 2012 15:15 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] Not able to continue with Equilibration Hi! I'm having a

AW: [gmx-users] Not able to continue with Equilibration

2012-03-29 Thread Rausch, Felix
good idea (search the mailing list for many discussions about this topic). Good luck. Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von Hendry Gesendet: Donnerstag, 29. März 2012 11:25 An: Discussion list for GROMACS users Betreff: [gmx-users] Not able to con

Re: [gmx-users] Not able to continue with Equilibration

2012-03-29 Thread Hendry
> > Good luck. > > ** ** > > *Von:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > *Im Auftrag von *Hendry > *Gesendet:* Donnerstag, 29. März 2012 11:25 > *An:* Discussion list for GROMACS users > *Betreff:* [gmx-users] Not able to continue with E

Re: [gmx-users] Not able to continue with Equilibration

2012-03-29 Thread Mark Abraham
On 29/03/2012 8:22 PM, Hendry wrote: Hi, I am using Gromacs 4.5.4. After successful minimization by SD, I continued with equilibration step but I got the below errors. I tried many times with different parameters but the problem still persists. I have given errors and md parameters of equili

Re: [gmx-users] Not able to continue with Equilibration

2012-03-29 Thread francesca vitalini
Hi! I'm having a similar problem. I have a dimer solvated in a big box of water plus ions that I have managed to minimize correctly (see output of minimization at the end) but when I try to run NVT equilibration (see later) I get LINCS warnings(see below) refearred to atoms which are not in a clust

AW: [gmx-users] Not able to continue with Equilibration

2012-03-29 Thread Rausch, Felix
reff: Re: [gmx-users] Not able to continue with Equilibration Hi! I'm having a similar problem. I have a dimer solvated in a big box of water plus ions that I have managed to minimize correctly (see output of minimization at the end) but when I try to run NVT equilibration (see later) I

Re: [gmx-users] Not able to continue with Equilibration

2012-03-29 Thread francesca vitalini
gured out why. > Maybe it's worth a try for you, too? > Cheers, > Felix > > -Ursprüngliche Nachricht- > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im > Auftrag von francesca vitalini > Gesendet: Donnerstag, 29. März 2012 15:15 > A

Re: [gmx-users] Not able to continue with Equilibration

2012-03-29 Thread Justin A. Lemkul
francesca vitalini wrote: Hallo Felix, thank you for your answer. I tried the constraints = h-bonds but no change in the output. If I look at the step.pdb file that is produced after the running I have some strange outcome. For example some of my atoms are not recognized as part of my protein a

Re: [gmx-users] Not able to continue with Equilibration

2012-03-29 Thread francesca vitalini
from "all-bonds" to only "h-bonds" > did the trick for me, although I never exactly figured out why. > Maybe it's worth a try for you, too? > Cheers, > Felix > > -Ursprüngliche Nachricht- > Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun

Re: [gmx-users] Not able to continue with Equilibration

2012-03-29 Thread Justin A. Lemkul
e, although I never exactly figured out why. Maybe it's worth a try for you, too? Cheers, Felix -Ursprüngliche Nachricht- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von francesca vitalini Gesendet: Donnerstag, 29. März 2012 15:15 An: Discussion

Re: [gmx-users] Not able to continue with Equilibration

2012-03-29 Thread francesca vitalini
t;>> ; Dispersion correction >>> DispCorr        = EnerPres      ; account for cut-off vdW scheme >>> ; Velocity generation >>> gen_vel         = yes           ; assign velocities from Maxwell >>> distribution >>> gen_temp        = 300           ; tem

Re: [gmx-users] Not able to continue with Equilibration

2012-03-29 Thread Mark Abraham
On 30/03/2012 8:39 AM, francesca vitalini wrote: Thank you Justin for your answer. I'm trying to add the position restraints to my protein, but I have a problem. My topology is made of a chain repeated twice and if I want to build the position restraints through genrestr from a gro file, the nume

Re: [gmx-users] Not able to continue with Equilibration

2012-03-30 Thread francesca vitalini
Dear Mark, Thank you for your answer. I'm trying now with the position restraints and see what happens. However, another question came up to my mind in the mean time. I'm using GROMACS 3.3.1 (version with mapping for reverse transformation, I have been posting on it before) and for the mdrun the fl

Re: [gmx-users] Not able to continue with Equilibration

2012-03-30 Thread Justin A. Lemkul
francesca vitalini wrote: Dear Mark, Thank you for your answer. I'm trying now with the position restraints and see what happens. However, another question came up to my mind in the mean time. I'm using GROMACS 3.3.1 (version with mapping for reverse transformation, I have been posting on it be