Re: [gmx-users] make_ndx

sarbani chattopadhyay wrote: hi, I want to select two groups in the index file, one group consisting of only the aromatic ring of phenylalanine and the other group consisting of only the alpha carbon. I want to know the way to use the make_ndx command for this. After entering

Re: Re: [gmx-users] make_ndx

 Thanks Mark, I could do it following your suggestion. Sarbani On Wed, 24 Oct 2007 Mark Abraham wrote : sarbani chattopadhyay wrote: hi, I want to select two groups in the index

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 gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org 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,

[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 and

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

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

[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

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

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

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 list

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? So,

[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