Re: [gmx-users] confusion about segmentation fault during mdrun

Lan Hua wrote: Hi Justin, I took all your suggestions. But the same thing happened again in the NPT step with the "Segmentation fault" for some starting structure. I attached the mdp file I used. Do you have any idea what else could cause this error? Thank you very much! The on

Re: [gmx-users] confusion about segmentation fault during mdrun

Hi Justin, I took all your suggestions. But the same thing happened again in the NPT step with the "Segmentation fault" for some starting structure. I attached the mdp file I used. Do you have any idea what else could cause this error? Thank you very much! Best, Lan On Wed, May 19, 2010

Re: [gmx-users] confusion about segmentation fault during mdrun

Thanks. The simulations are regular MD in explicit water at room temperature. Lan On Wed, May 19, 2010 at 6:03 PM, Justin A. Lemkul wrote: > > > Lan Hua wrote: > >> Hi Justin, >> >> I appreciated your quick answers. So if I understand correctly, using >> constraints = hbonds with the time

Re: [gmx-users] confusion about segmentation fault during mdrun

Lan Hua wrote: Hi Justin, I appreciated your quick answers. So if I understand correctly, using constraints = hbonds with the time step of 2fs, it should be fine, right? Maybe. If your goal is REMD (I'm not clear from your original post) then stability may be an issue at higher tem

Re: [gmx-users] confusion about segmentation fault during mdrun

Hi Justin, I appreciated your quick answers. So if I understand correctly, using constraints = hbonds with the time step of 2fs, it should be fine, right? Thanks, Lan On Wed, May 19, 2010 at 3:52 PM, Justin A. Lemkul wrote: > > > Lan Hua wrote: > >> Hi Justin, >> >> Thank you so much for

Re: [gmx-users] confusion about segmentation fault during mdrun

Lan Hua wrote: Hi Justin, Thank you so much for your quick reply and good suggestions. The following is my answer. On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul > wrote: Lan Hua wrote: Hi All, I understand that the error of segm

Re: [gmx-users] confusion about segmentation fault during mdrun

Hi Justin, Thank you so much for your quick reply and good suggestions. The following is my answer. On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul wrote: > > > Lan Hua wrote: > >> Hi All, >> >> I understand that the error of segmentation fault may come from many >> reasons, but I ju

Re: [gmx-users] confusion about segmentation fault during mdrun

Lan Hua wrote: Hi All, I understand that the error of segmentation fault may come from many reasons, but I just couldn't figure out the reason of this error in my simulations. I want to run md simulations with explicit water for 20 structures of one domain (residue 77-148) of calmodu

[gmx-users] confusion about segmentation fault during mdrun

Hi All, I understand that the error of segmentation fault may come from many reasons, but I just couldn't figure out the reason of this error in my simulations. I want to run md simulations with explicit water for 20 structures of one domain (residue 77-148) of calmodulin (PDB 1CFC). These