Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread Mark Abraham
That looks like (at least) a grompp bug leading to the error. Can you attach a .tpr file to http://redmine.gromacs.org/issues/1164 please Francesco? Mark On Tue, Feb 26, 2013 at 8:09 PM, Justin Lemkul wrote: > > > On 2/26/13 2:06 PM, francesco oteri wrote: > >> I downloaded and installed gromac

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread Justin Lemkul
On 2/26/13 2:06 PM, francesco oteri wrote: I downloaded and installed gromacs-4.6 but I get the warning WARNING 1 [file NVE.mdp]: The sum of the two largest charge group radii (0.067845) is larger than rlist (1.20) - rvdw (1.20) I attacch the files you may need to solve the prob

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread francesco oteri
I downloaded and installed gromacs-4.6 but I get the warning WARNING 1 [file NVE.mdp]: The sum of the two largest charge group radii (0.067845) is larger than rlist (1.20) - rvdw (1.20) I attacch the files you may need to solve the problem NVE.mdp

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread francesco oteri
Thank you so much for the help! 2013/2/26 Justin Lemkul > > > On 2/26/13 12:01 PM, francesco oteri wrote: > >> I am using 4.5.5...Is it OK? >> >> > If it's giving a note about that, then clearly not. Try 4.6. But as I > said, there's nothing actually wrong. > > -Justin > > >> 2013/2/26 Justin

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread Justin Lemkul
On 2/26/13 12:01 PM, francesco oteri wrote: I am using 4.5.5...Is it OK? If it's giving a note about that, then clearly not. Try 4.6. But as I said, there's nothing actually wrong. -Justin 2013/2/26 Justin Lemkul On 2/26/13 11:47 AM, francesco oteri wrote: Thank you Justin, I

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread francesco oteri
I am using 4.5.5...Is it OK? 2013/2/26 Justin Lemkul > > > On 2/26/13 11:47 AM, francesco oteri wrote: > >> Thank you Justin, >> I added >> rlistlong = 1.4 >> >> but still grompp complains: >> NOTE 1 [file 02md.mdp]: >>For energy conservation with switch/shift potentials, rlist should

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread Justin Lemkul
On 2/26/13 11:47 AM, francesco oteri wrote: Thank you Justin, I added rlistlong = 1.4 but still grompp complains: NOTE 1 [file 02md.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. Why doesn't grompp looks for rlistlong va

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread francesco oteri
Thank you Justin, I added rlistlong = 1.4 but still grompp complains: NOTE 1 [file 02md.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. Why doesn't grompp looks for rlistlong value? Francesco 2013/2/26 Justin Lemkul > > >

Re: [gmx-users] Implementation of CHARMM setup in GROMACS

2013-02-26 Thread Justin Lemkul
On 2/26/13 11:30 AM, francesco oteri wrote: Dear gromacs users, in Bjelkmar et al. (2010) where the implementation of CHARMM in GROMACS is described, the authors say that: "Electrostatics was treated with particle-mesh Ewald (PME), using a short-range cutoff of 1.2 nm, and van der Waals intera