Re: [gmx-users] table-extension in mdp ?!

  On January 17, 2011 at 4:32 PM jojo J wrote: Dear users, Please help me with the following problem. My simulation is crashing for an unstability reason I guess. Can you please help me what wrong is exaclty. I had done the

[gmx-users] table-extension in mdp ?!

Dear users, Please help me with the following problem. My simulation is crashing for an unstability reason I guess. Can you please help me what wrong is exaclty. I had done the simulation with exactly the same input files but with version 4.0.7 and never got this error. Thanks for your comments.

RE: [gmx-users] table extension

, or zero: fine, no artifacts, or 10^30: immediate crash of mdrun). Berk Date: Thu, 27 Aug 2009 17:18:13 +0300 Subject: Re: [gmx-users] table extension From: omer...@gmail.com To: gmx-users@gromacs.org But what if the gmx code did notice it? Koby Levy research group, Weizmann Institute of Science

Re: [gmx-users] table extension

But what if the gmx code did notice it? Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Aug 27, 2009 at 16:21, Mark Abraham wrote: > It would look up a non-random energy and force. If the code never noticed

Re: [gmx-users] table extension

Omer Markovitch wrote: Thanks. And what happens if later on it comes back to the cut-off + table-extension range? It would look up a non-random energy and force. If the code never noticed the distance was out-of-range, it won't notice it come back into range either. Mark Koby Levy researc

Re: [gmx-users] table extension

Thanks. And what happens if later on it comes back to the cut-off + table-extension range? Koby Levy research group, Weizmann Institute of Science. FAX: 972-77-444-7905 http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Thu, Aug 27, 2009 at 11:13, Berk Hess wrote: > A interaction beyond the c

RE: [gmx-users] table extension

Hi, No, this is not correct. A interaction beyond the cut-off + table-extension will get a random energy and force depending on what is stored in the memory of your computer beyond the table___ gmx-users mailing listgmx-users@gromacs.org http://lis

Re: [gmx-users] table extension

Thanks Mark. I am simulating a dimer in vacuum, and it is my understanding that once a non-bonded interaction has exceeded the table-extension cutoff this interaction will NOT be included in the potential for the remaining simulation, even if it will later come back to a distance within the table-e

Re: [gmx-users] table extension

Omer Markovitch wrote: Dear GMXs, I would like to clear something out, for myself: The table extension given in MDP file applies to "nonbond_params" & "pairs" interactions which are specified in the TOP file (and also electrostatics)? From 7.3.12, yes. These are the nonbonded interactions. Is

[gmx-users] table extension

Dear GMXs, I would like to clear something out, for myself: The table extension given in MDP file applies to "nonbond_params" & "pairs" interactions which are specified in the TOP file (and also electrostatics)? Is there an interaction which does not use the table extension (other then bonds, angle

Re: [gmx-users] table-extension

> *hi ! > I am getting this error with regard to table extensions. Any suggestions > to > overcome this would be greatly appreciated! > Thanks > Jayant James > * > Warning: 1-4 interaction between 429 and 434 at distance 1.002 which is > larger than the 1-4 table size 1.000 nm > These are ignored f

[gmx-users] table-extension

*hi ! I am getting this error with regard to table extensions. Any suggestions to overcome this would be greatly appreciated! Thanks Jayant James * Warning: 1-4 interaction between 429 and 434 at distance 1.002 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the s