[gmx-users] histidine (HISB) planarity

Hi Folks, First just want to say thanks to all of those who have responded to my previous questions. I belong to a couple different bb's relating to the various software packages I use, and I have to say this one seems to have the lowest number of unanswered questions (from all users, that is, no

Re: Fwd: [gmx-users] Hen egg white lysozyme.

Hi David.I thought of the same and I started running it using angular mode yesterday.Thanks though for a quick feedback.-VissuOn 8/11/06, David van der Spoel <[EMAIL PROTECTED]> wrote:Viswanadham Sridhara wrote: > Hello everyone,> I could figure out that parameters for NAG are not that important.

Re: Fwd: [gmx-users] Hen egg white lysozyme.

Viswanadham Sridhara wrote: Hello everyone, I could figure out that parameters for NAG are not that important. So, I used free HEWL. I started running it, but I realize that the protein started to rotate around the center of mass with a frequency of around 200ps. I used "Linear" as an option fo

Fwd: [gmx-users] Hen egg white lysozyme.

Hello everyone,I could figure out that parameters for NAG are not that important. So, I used free HEWL.I started running it, but I realize that the protein started to rotate around the center of mass with a frequency of around 200ps. I used "Linear" as an option for comm_mode and I used "Protein" i

Re: [gmx-users] amide/imidic acid transition in Asparagine

Jiancong Xu wrote: hey guy, have anyone ever worked with an imidic acid form of asparagine (i.e. with the side chain of -C(OH)=NH)? If you'd share a force field file with me, that'd be great. Thanks alot, we have done a protonated Gln, i.e. -C(OH)=NH2, that is now in the CVS for 3.3.1. Jianco

[gmx-users] amide/imidic acid transition in Asparagine

hey guy, have anyone ever worked with an imidic acid form of asparagine (i.e. with the side chain of -C(OH)=NH)? If you'd share a force field file with me, that'd be great. Thanks alot, Jiancong\ - Jiancong Xu Graduate Student Department of Ch

Re: [gmx-users] Fene and Quartic Potential

PAUL NEWMAN wrote: Dear all: I want to use Fene Potential and Quartic Angle Potential which both are available in the new gromacs version 3.3 . What I want to know is how can I set up the parameters for these potential in my *.itp file. Ok my try is here. Are the possition of the parameters o

[gmx-users] Fene and Quartic Potential

Dear all: I want to use Fene Potential and Quartic Angle Potential which both are available in the new gromacs version 3.3 . What I want to know is how can I set up the parameters for these potential in my *.itp file. Ok my try is here. Are the possition of the parameters ok? and Are the number

[gmx-users] Ploting xvg file in R statistic package

Hi all, Anyone know , to convert xvg formated data of gromacs for analysis in R statistical package. with thanks ! B.Nataraj -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A no graphics, no pop-ups email service ___ gmx-users mailing list

[gmx-users] Re: g_hbond

Hi David, Thank you for the explanation. Regards, Jian Zou - Original Message - Date: Fri, 11 Aug 2006 08:24:54 +0200 From: David van der Spoel <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Re: g_hbond To: Discussion list for GROMACS users Message-ID: <[EMAIL PROTECTED]> Content-Type:

Re: [gmx-users] Box is exploding!

Absalom Zamorano wrote: Hi gromacs people, Im unfolding a protein over 525K, but simulation is stoped and in the log file appears "WARNING: your box is exploding!", has someone idea about it?, Are there some parameter to modify? I will appreciate very much your help. Due to temperature the sy

[gmx-users] Box is exploding!

Hi gromacs people, Im unfolding a protein over 525K, but simulation is stoped and in the log file appears "WARNING: your box is exploding!", has someone idea about it?, Are there some parameter to modify? I will appreciate very much your help. Thanks for advance. Dr. Absalom Zamorano Carrillo Prof