Re: [gmx-users] position restraints

Resending my previous email, since earlier one failed for curious reason... On Thu, Jan 2, 2014 at 4:21 PM, Chetan Mahajan wrote: > Thanks for all the replies. Yes, missing underscore was the problem. It's > solved. > Thanks > Chetan > > > On Thu, Jan 2, 2014 at 2:48 PM, wrote: > >> Hi, >> It

Re: [gmx-users] gmx user forum not accessible

On 1/5/14, 8:01 PM, Christian Wagner wrote: Hi All, After I logged in, I tried to access information (http://lists.gromacs.org/pipermail/gmx-users/2013-March/079219.html) from the gmx users archive and get the following error: Not Found The requested URL /pipermail/gmx-users/2013-March/079

[gmx-users] gmx user forum not accessible

Hi All, After I logged in, I tried to access information (http://lists.gromacs.org/pipermail/gmx-users/2013-March/079219.html) from the gmx users archive and get the following error: Not Found The requested URL /pipermail/gmx-users/2013-March/079219.html was not found on this server. Apache/

[gmx-users] questions about Topolbuild

Dear all Can someone help us about how to add misssing parameters into Topolbuild? We are using topolbuild to build *top file for a molecular which has a amide group. It is strange for the same atom types. Some atoms' potential can be assigned by Topolbuild but some can not. Topolbuld reports mi

[gmx-users] Simulating a 282 atom molecule. How do I split it into parts?

I have this molecule I want to simulate: http://pastebin.com/raw.php?i=7bsWKjU3 I have tried using acpype on the whole thing to obtain the needed .itp and .gro, but it takes a couple days to finish and I get errors because I do not have enough memory. I was wondering if splitting this molecule in

Re: [gmx-users] electrical potential using Gromacs

Hi Fereshte, I used PME. Andrew -Original Message- From: Fereshte Taherian [mailto:tab...@csi.tu-darmstadt.de] Sent: Saturday, January 04, 2014 5:29 PM To: Andrew DeYoung Subject: RE: electrical potential using Gromacs Hi Andrew, Many Thanks for your reply. I am checking my system bas

Re: [gmx-users] simulation using tabulated dihedral potentials.

On Sun, Jan 5, 2014 at 5:51 AM, Chandan Choudhury wrote: > On Sat, Dec 28, 2013 at 5:24 AM, Justin Lemkul wrote: > > > > > > > On 12/27/13, 12:58 AM, Chandan Choudhury wrote: > > > >> Dear Justin and Mark, > >> > >> Thanks for the reply. I have regenerated the potentials for the bonded > and > >

Re: [gmx-users] position restraints

Thanks for all the replies. Yes, missing underscore was the problem. It's solved. Thanks Chetan On Thu, Jan 2, 2014 at 2:48 PM, wrote: > Hi, > It seems you are missing the underscore between position & restraints in > the directive. > Check your code again. > > -Original Message- > From