RE: [gmx-users] missing Ryckaert-Bell in 3.3.2 is now considered asERROR?

From: Martin Höfling <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion list for GROMACS users Subject: [gmx-users] missing Ryckaert-Bell in 3.3.2 is now considered asERROR? Date: Wed, 24 Oct 2007 00:14:55 +0200 Hi all, has the default behaviour of 3.3.1 -> 3

[gmx-users] surface tension calculation in g_energy

Hi all, I use the option "#Surf*SurfTens" in g_engery to calculate the surface tension, but I find that I really do not know how it works after I get some inconsistent results compared with the calculation using the formula "gamma = 0.5*(Pzz - (Pxx+Pyy)/2) * Lz" ( there are two surfaces here an

Re: [gmx-users] surface tension calculation in g_energy

Bo Zhou wrote: Hi all, I use the option “#Surf*SurfTens” in g_engery to calculate the surface tension, but I find that I really do not know how it works after I get some inconsistent results compared with the calculation using the formula “gamma = 0.5*(Pzz - (Pxx+Pyy)/2) * Lz” ( there ar

Re: [gmx-users] g_rmsf and pbc

I tried "trjconv -pbc nojump" to the whole protein and then calculated the rmsf of the subunits. This method seems good to some separate subunits, but other separate subunits still have strange high rmsf values. I try "trjconv -pbc mol" too, and i have got same results. In this simulation,the subu

[gmx-users] reference for urea.itp

Does anyone know the reference for the parameters for urea in the urea.itp file (found in the top directory)? Thanks, Ronen ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive

Re: [gmx-users] alpha Carbon-Aromatic ring hydrogen bond

Hi Sarbani, If I understand correctly your problem, you want to know hydrogen bond between center of the aromatic ring and CA hydrogen atom with time, you can do this in two steps (if you are not considering angle criteria). 1) first create the index files which should have two extra groups fi

Re: [gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ?

Hello Maria, You can do it by two different methods. 1) You can increase the default VdW radii of the lipid atoms in /usr/local/gromacs/share/top/vdwradii.dat file (path might be different from your system), say 0.5 for carbon, so genbox will not add the water inside the bilayer. but you will

Re: [gmx-users] reference for urea.itp

[EMAIL PROTECTED] wrote: Does anyone know the reference for the parameters for urea in the urea.itp file (found in the top directory)? Please don't use it as is. Check literature for better models. Thanks, Ronen ___ gmx-users mailing listgmx

Re: [gmx-users] reference for urea.itp

Thanks. I am looking at other models as well, but was wondering how the numbers in urea.itp were obtained. What type of properties they were parametrized for? Ronen -- Original message -- From: David van der Spoel <[EMAIL PROTECTED]> > > [EMAIL PROTECTED] wrote:

Re: [gmx-users] reference for urea.itp

[EMAIL PROTECTED] wrote: Thanks. I am looking at other models as well, but was wondering how the numbers in urea.itp were obtained. What type of properties they were parametrized for? none. just copied from the gromos 87 ff. Ronen -- Original message -- From:

[gmx-users] g_energy has no bond entry when MD analysis

Dear friends: when my MD was finished and I want to analyse the bond energy of the protein ,but g_energy did not show bond entry: the first entry is angle? When energy miniumzation finished,g_energy did show G96 bond. why? Please help me! Thank you! -

Re: [gmx-users] g_energy has no bond entry when MD analysis

> Dear friends: > when my MD was finished and I want to analyse the bond energy of the > protein ,but g_energy did not show bond entry: the first entry is angle? > When energy miniumzation finished,g_energy did show G96 bond. why? So, when did you use bond length constraints? What effect would

回复： Re: [gmx-users] g_energy has no bond entry when MD analysis

Yes, I use bond constraints! Mark Abraham <[EMAIL PROTECTED]> 写道： > Dear friends: > when my MD was finished and I want to analyse the bond energy of the > protein ,but g_energy did not show bond entry: the first entry is angle? > When energy miniumzation finished,g_energy did show G96 bond. why?

[gmx-users] solvate using genbox results in water in the center ofthe bilayer. How to edit pdb file contents in gromacs ?

You can do it by two different methods. 1) You can increase the default VdW radii of the lipid atoms in /usr/local/ gromacs/share/top/vdwradii.dat file (path might be different from your system), say 0.5 for carbon, so genbox will not add the water inside the bilayer. Cleaner method is to:

Re: [gmx-users] solvate using genbox results in water in the centerofthe bilayer. How to edit pdb file contents in gromacs ?

Dear Chris, Thanks for your time and suggestion. I tried all the possible pressure couplings (including semiisotropic) and run it for around 500ps.Gap between head group and water molecule disappear, but I was getting uneven distribution of water molecules. I am pasting my previous mail again.