Re: [gmx-users] step 0Segmentation fault: 11

2013-11-28 Thread Mark Abraham
Huge forces lead to crazy displacements whose next forces are looked up outside the boundaries of your table, which leads to a segmentation fault. GROMACS doesn't waste its time checking for this, since that would hurt everyone's performance and gain only a descriptive error that something is

Re: [gmx-users] step 0Segmentation fault: 11 (Mark Abraham)

2013-11-28 Thread ERASTOVA V.
Thank you, Mark. It makes sense. I am using FF developed by other group, that was run in Discover before. I am not sure I like how the plots of potentials look. V Huge forces lead to crazy displacements whose next forces are looked up outside the boundaries of your table, which leads to a

Re: [gmx-users] step 0Segmentation fault: 11

2013-11-27 Thread Valentina
Thank you for your reply. I am now suspecting charges to be a problem. -- View this message in context: http://gromacs.5086.x6.nabble.com/step-0Segmentation-fault-11-tp5012832p5012857.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list *

Re: [gmx-users] step 0Segmentation fault: 11

2013-11-27 Thread Mark Abraham
Start with the simplest relevant system (e.g. two atoms with no bond). Then two atoms with bond. Then more complex. Now you have a chance of seeing what is wrong - particularly if there might be multiple things wrong! Mark On Wed, Nov 27, 2013 at 4:29 PM, Valentina

Re: [gmx-users] step 0Segmentation fault: 11

2013-11-27 Thread Valentina
I still cannot resolve this problem. Is there any way to find out what is causing Segmentation Fault? Normally Gromacs provides quite comprehendible errors, but this one. I have checked the charges against DFT. I also have the output of the system simulated with Discover. I am using that force

Re: [gmx-users] step 0Segmentation fault: 11

2013-11-27 Thread Justin Lemkul
On 11/27/13 7:30 PM, Valentina wrote: I still cannot resolve this problem. Is there any way to find out what is causing Segmentation Fault? Normally Gromacs provides quite comprehendible errors, but this one. I have checked the charges against DFT. I also have the output of the system