Re: [gmx-users] step size too small

Minnale, Please do read the following: http://wiki.gromacs.org/index.php/Errors This one's in there. Tsjerk On Mon, Jun 30, 2008 at 11:26 AM, minnale <[EMAIL PROTECTED]> wrote: > > Hi all, > 1) I have embedded protein into popcbilayer > 2) Energy minimisation > 3) Later added ions by usin

[gmx-users] step size too small

Hi all, 1) I have embedded protein into popcbilayer 2) Energy minimisation 3) Later added ions by using genion, 4) When I am trying to run minimisation its showing following sentences Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested p

RE: [gmx-users] Step size too small

is and was able to move on with EM and simulation. Rgds John > From: [EMAIL PROTECTED]> Subject: Re: [gmx-users] Step size too small> Date: > Mon, 20 Aug 2007 10:07:09 +0200> To: gmx-users@gromacs.org> > > 17 aug 2007 > kl. 21.46 skrev TJ Piggot:> > > Hi,>

Re: [gmx-users] Step size too small

17 aug 2007 kl. 21.46 skrev TJ Piggot: Hi, I do not think that what Per suggests is the problem, if you look at the potential energy after the minimisation this value is huge (and the other two values are inf!). The problem is most likely with your topology. As you say the two molecules

Re: [gmx-users] Step size too small

Hi, I do not think that what Per suggests is the problem, if you look at the potential energy after the minimisation this value is huge (and the other two values are inf!). The problem is most likely with your topology. As you say the two molecules have been successfully minimised on their own

Re: [gmx-users] Step size too small

Hello! Check out http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small. 2C_or_no_change_in_energy._Converged_to_machine_precision. 2C_but_not_to_the_requested_precision Cheers /Per 17 aug 2007 kl. 18.28 skrev Sheyore Omovie: Dear gmx-users, I have 2 molecules in a box, as usual pdb2

[gmx-users] Step size too small

Dear gmx-users, I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited the .top file to remove the bonds created between the two molecules, I also added a distance restraint btw the molecules. (The 2 structures have been separately minimized). However, I get the ff message fo