Re: [gmx-users] Structure optimization failure

2012-07-01 Thread Mark Abraham
On 30/06/2012 10:18 PM, ms wrote: On 29/06/12 19:59, Justin A. Lemkul wrote: Wouldn't it be nice to create a table of "standard settings" for each forcefield in the gmx documentation (with lit references of course)? Well, anyone is welcome to submit anything they feel would be useful... ;)

Re: [gmx-users] Structure optimization failure

2012-06-30 Thread ms
On 29/06/12 19:59, Justin A. Lemkul wrote: Wouldn't it be nice to create a table of "standard settings" for each forcefield in the gmx documentation (with lit references of course)? Well, anyone is welcome to submit anything they feel would be useful... ;) I have considered this in the past,

Re: [gmx-users] Structure optimization failure

2012-06-29 Thread Justin A. Lemkul
On 6/29/12 11:10 AM, massimo sandal wrote: On 29 Jun 2012 15:09, "Justin A. Lemkul" mailto:jalem...@vt.edu>> wrote: > > > > On 6/29/12 9:04 AM, massimo sandal wrote: >> >> >> On 29 Jun 2012 14:08, "Justin A. Lemkul" mailto:jalem...@vt.edu>

Re: [gmx-users] Structure optimization failure

2012-06-29 Thread Justin A. Lemkul
On 6/29/12 9:04 AM, massimo sandal wrote: On 29 Jun 2012 14:08, "Justin A. Lemkul" mailto:jalem...@vt.edu>> > > The settings in my tutorial are for use with OPLS-AA and are thus not suitable for a simulation with CHARMM. Cutoffs and other aspects will be different. This is interesting. In

Re: [gmx-users] Structure optimization failure

2012-06-29 Thread Justin A. Lemkul
On 6/29/12 8:04 AM, Lara Bunte wrote: Hi Thank you for the fast answer :-) I use a tip3p water model. I wrote spc216 because this is what I am using with genbox. My mistake. Now I used the equilibrating file out of this tutorial: http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tuto

Re: [gmx-users] Structure optimization failure

2012-06-29 Thread Lara Bunte
same problem. The water could not be settled. What is wrong with this file for my system? Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 12:23 Freitag, 29.Juni 2012 Betreff: Re: [gmx-users] Structure

AW: [gmx-users] Structure optimization failure

2012-06-29 Thread Rausch, Felix
- Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im Auftrag von Lara Bunte Gesendet: Freitag, 29. Juni 2012 12:03 An: gmx-users@gromacs.org Betreff: [gmx-users] Structure optimization failure Hello I use a CHARMM27 force field and my system is lumiflavin in water. I

Re: [gmx-users] Structure optimization failure

2012-06-29 Thread Justin A. Lemkul
On 6/29/12 6:01 AM, Lara Bunte wrote: Hello I use a CHARMM27 force field and my system is lumiflavin in water. I use the spc216 water model, a dodecahedral box with 1.3 nm. I want to make a CHARMM27 should be combined with TIP3P, not SPC. structure minimization. I made a file pr.mdp. Could

[gmx-users] Structure optimization failure

2012-06-29 Thread Lara Bunte
Hello I use a CHARMM27 force field and my system is lumiflavin in water. I use the spc216 water model, a dodecahedral box with 1.3 nm. I want to make a structure minimization. I made a file pr.mdp. Could you please tell me, what I could do better in this file, or what is wrong? I guess there ha