[gmx-users] GROMACS 4.5.4 keep crashing all the time

he list. Use thewww interface or send it to gmx-users-request aGROMACS 4.5.4 keep crashing all the time Tsjerk Wassenaar tsjerkw at gmail.com Thu Sep 1 15:48:40 CEST 2011 * Previous message: [gmx-users] GROMACS 4.5.4 keep crashing all the time * Next message: [gmx-users] Non-zero total char

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

time Tsjerk Wassenaar tsjerkw at gmail.com Thu Sep 1 15:48:40 CEST 2011 * Previous message: [gmx-users] GROMACS 4.5.4 keep crashing all the time * Next message: [gmx-users] Non-zero total charge * Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Hi Chris, I can ima

[gmx-users] GROMACS 4.5.4 keep crashing all the time

erface or send it to gmx-users-request aGROMACS 4.5.4 keep crashing all the time Tsjerk Wassenaar tsjerkw at gmail.com Thu Sep 1 15:48:40 CEST 2011 * Previous message: [gmx-users] GROMACS 4.5.4 keep crashing all the time * Next message: [gmx-users] Non-zero total charge * Messages

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Chris, I can imagine that the pressure scaling has a more profound effect on the 'visible' surroundings if a cut-off is used, while this will not be the case when using PME. So the shock for an atom when the coordinates are adjusted can be expected to be greater with cut-off based methods, rend

[gmx-users] GROMACS 4.5.4 keep crashing all the time

I am glad that the pressure coupling intervals have been identified as a source of instability for poorly equilibrated systems as I was unaware of that. Still, the fact that the SD integrator also solves the problem also suggests that this is simply a poorly equilibrated system. I am not su

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

On 1/09/2011 6:32 PM, Itamar Kass wrote: Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Equilibrating with NVT before NPT c

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Itamar, Yes, it appears that the 4.5.x series is more sensitive, due to the pressure coupling at intervals rather than at every step. Unfortunately the way it is now tied in with calculations of energies and neighbour searching indeed means that having nstpcouple set at 1 results in low simulat

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Tsjerk, Thanks for the help, it actually worked. When nstpcouple is set to 1m the system can be equilibrated (NPT) without LINCS error. I hadn't thought about it as I never use NVT (unless doing FE calculations). Is this mean the 4.5.4 is more sensitive the 4.0.7? Is this effect the data c

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Itamar, I haven't really followed the discussion and I'm a bit too lazy to look it all up now ;) But have you tried setting the nst parameters to 1 (except for output). Especially nstpcouple. Note that nstpcouple=1 requires nstlist=1 and nstcalcenergy=1. If that solves the problem, you may nee

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

HI Chris, I am sorry that from my mails it is seems like I am not appreciate the help, because I appreciate it much. It is just the fact that I am trying to give as much info as I can and to go over any idea in the mailing list without actually delay my other stuff. So again, I wish thanks for

[gmx-users] GROMACS 4.5.4 keep crashing all the time

Itamar: We really are trying to help. I think that perhaps you don't grasp how difficult it is to help without being able to access the simulation directly. Therefore we have ideas and we ask you to do specific things that are going to move us toward a solution, either by finding answers

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Justin, I did repeat it using gen_val and running temperature the same, with no effect, it is still crash. I didn't replied point #6 because the atoms which triggers the LINCS are different between each try. Sometimes it is the peptide N and H, like in the case of 981 and 982, and sometimes

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Itamar Kass wrote: Hi Mark, I didn't had the time to do the SD yet, but serial run end with the same results. I didn't try water only system, as this is of no interest to me, but I will simplify the system later on. Being of interest to you and being a useful diagnostic may be different.

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Mark, I didn't had the time to do the SD yet, but serial run end with the same results. I didn't try water only system, as this is of no interest to me, but I will simplify the system later on. Cheers, Itamar On 01/09/2011, at 10:51 AM, Mark Abraham wrote: > On 1/09/2011 10:20 AM, Itamar K

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

On 1/09/2011 10:20 AM, Itamar Kass wrote: Hi Chris, Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again the simulations had stopped after 1000 LINCS error (I can extend the simulations using 4.0.

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Chris, Thanks for the email, I am sorry it took me some time to replay. I tried 4.5.4 again, now starting from a 5 ns simulations run using 4.0.7, and again the simulations had stopped after 1000 LINCS error (I can extend the simulations using 4.0.7). I know that gromacs stopped after 1000

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

My apologies; the remainder of the thread in which these suggestions were already proposed and discussed showed up where I didn't expect them. Sorry to repeat what's already been said. MZ On Thu, Aug 18, 2011 at 12:58 PM, Matthew Zwier wrote: > Hi Itamar, > > In my experience, the 4.5 series ap

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

Hi Itamar, In my experience, the 4.5 series appears to be slightly less tolerant of unstable systems than the 4.0 series. Try minimizing and/or equilibrating your system longer. See http://www.gromacs.org/Documentation/Errors and http://www.gromacs.org/Documentation/Terminology/Blowing_Up MZ

[gmx-users] GROMACS 4.5.4 keep crashing all the time

OK, here's my last few ideas: 1. Please try to repeat this with gen_vel set to the same value as your temperature coupling 2. Can you reproduce this in serial? 3. Can you reproduce this with the sd integrator? 4. Can you reproduce this with a simpler system? protein in vacuum or just wate

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

Hi Chris, thanks for the advice, I have to say I tried this as well without any success. Itamar On 18/08/2011, at 11:11 AM, chris.ne...@utoronto.ca wrote: > run an EM with flexible water. I often find that this is the only way to get > a stable system. 500 steps of steep with define=-DFLEXIBLE

[gmx-users] GROMACS 4.5.4 keep crashing all the time

run an EM with flexible water. I often find that this is the only way to get a stable system. 500 steps of steep with define=-DFLEXIBLE (or different depending on your water model I think) should be enough. Chris. Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: c

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

Hi Justing, I had reinitialised the systems after the PR run but I don't think this is the origin of the error. Because the system with the Ca crashed allways in the PR state, although the systems run with 4.0.7 done it fine. Best, Itamnar On 18/08/2011, at 10:39 AM, Justin A. Lemkul wrote: >

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

Dear Mark, We also tried to minimise the system in vacuum before adding water and ions withou, but it still crashed when we did MD. Itamar. On 18/08/2011, at 10:31 AM, Mark Abraham wrote: > On 18/08/2011 10:14 AM, Itamar Kass wrote: >> >> Hi Chris and Justin, >> >> On 18/08/2011, at 9:36 AM

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

I concur with what Mark suggested about in vacuo EM. I would also point out the following problem(s): and the md.mdp: Here you call for 300 K as the reference temperature and the temperature at which you've equilibrated: tc-grps = Protein Non-Protein tau-t

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

On 18/08/2011 10:14 AM, Itamar Kass wrote: Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: chris.ne...@utoronto.ca wrote: You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste th

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

Hi Chris and Justin, On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: > > > chris.ne...@utoronto.ca wrote: >> You'll need to provide a much better report than this if you want to receive >> any useful help. >> Copy and paste the exact commands of what you did >> Copy and paste the exact log

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

chris.ne...@utoronto.ca wrote: You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages I'd also add that we need a detailed description of the system

[gmx-users] GROMACS 4.5.4 keep crashing all the time.

You'll need to provide a much better report than this if you want to receive any useful help. Copy and paste the exact commands of what you did Copy and paste the exact log file and error messages Do this for 4.0.7 and 4.5.4, for which I trust that you have been using exactly identical test

Re: Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, August 22, 2011. For all questions about CloudBroker and the CloudBroker Platfor

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

Hi Matthew, Thanks for the reply. First, I don't thinks it is poorly compiled bin, as I used both GROMACS compiled by me (on my machine) or by the sys-admin on Linux cluster or blue-gene. The simulations using 4.5.4 crashed giving LINCS error, which is not the case with 4.0.7 (using the same mdp

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

Could be a system blowing up, or perhaps a mis-compiled binary. What error messages do you get when the crash occurs? On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass wrote: > Hi all GROMACS useres and developers, > > I am interesting in simulating a small protein (~140 aa) in water, with and > wit

[gmx-users] GROMACS 4.5.4 keep crashing all the time.

Hi all GROMACS useres and developers, I am interesting in simulating a small protein (~140 aa) in water, with and without Ca ions. In order to do so, I had used version 4.5.4. I had solvate the protein in water, add ions to naturalise the systems, equilibrated the systems and then tried product