Re: [gmx-users] g_sas Vdwradii.dat

maite lopez cabezas wrote: Hi: Thanks for the quickly answer. The problem is like David said. g_sas use the Van der Waals radius of the vdwradii.dat file. I want to use the same valors that appear in this file but i want to know where they were taken for adding the P valor. Thanks, Maité

Re: [gmx-users] analysis of different groups with g_energy

Peyman Yamin wrote: Hi again, Now I remember! some old g_energy let me use numbers as the input for the terms I wanted...! Yeah, it changed going from 3.3 to 3.3.1, IIRC. This allowed for scripts to be much more general, since the numbers used to change for different simulation types. As

Re: [gmx-users] analysis of different groups with g_energy

Peyman Yamin wrote: Thanks! I had somewhere in my mind a memory of seeing an interactive g_energy some time ago, but it could be another version of it or that place in my mind would need a defragmentation! comments helped indeed anyway. If group X is one molecule, you would know from it's e

Re: [gmx-users] how to distancing the counter ions from the protein?

jayant james wrote: Hi! I had to incorporate a salt conc of 0.15M NaCl and once I have them in put in the the box,via genion, I find that they are in close proximity to the protein. Is it possible to keep them away from the protein because I do not want them so close !! What about your syste

Re: [gmx-users] analysis of different groups with g_energy

Hi again, Now I remember! some old g_energy let me use numbers as the input for the terms I wanted...! As you say, it looks like the total energy for different groups is not calculated. So I should somehow do it myself? If yes, I don't even know where I should get the terms I should add togeth

[gmx-users] how to distancing the counter ions from the protein?

Hi! I had to incorporate a salt conc of 0.15M NaCl and once I have them in put in the the box,via genion, I find that they are in close proximity to the protein. Is it possible to keep them away from the protein because I do not want them so close !! Thanks Jayant -- Jayasundar Jayant James www

Re: [gmx-users] analysis of different groups with g_energy

Thanks! I had somewhere in my mind a memory of seeing an interactive g_energy some time ago, but it could be another version of it or that place in my mind would need a defragmentation! comments helped indeed anyway. If group X is one molecule, you would know from it's energy, i.e. the sum of

Re: [gmx-users] g_sas Vdwradii.dat

Hi: Thanks for the quickly answer. The problem is like David said. g_sas use the Van der Waals radius of the vdwradii.dat file. I want to use the same valors that appear in this file but i want to know where they were taken for adding the P valor. Thanks, Maité On Sat, Jun 7, 2008 at 4:50 PM, Dav

Re: [gmx-users] analysis of different groups with g_energy

Peyman Yamin wrote: On Monday 09 June 2008 16:19, Justin A. Lemkul wrote: Well, ofcourse I did! otherwise I wouldn't expect any program to know them by itself! the problem is that I say: Well, there's a lesson here. You should spell out all relevant data - like your usage of energy groups in

Re: [gmx-users] TEE-REX installation error

TJ Piggot wrote: Hi, I am trying to install the TEE-REX patch for gromacs 3.3.1 and am getting the following make error: cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused

Re: [gmx-users] extract conformations !!

Anamika Awasthi wrote: Dear Friends, I want to extract conformations of each 1 ns from my 10 ns simulation. My this job is running for 20 ns, so shall I first stop my job and then do this? That won't be necessary, but there's no particular guarantee that all of your files are

[gmx-users] TEE-REX installation error

Hi, I am trying to install the TEE-REX patch for gromacs 3.3.1 and am getting the following make error: cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loo

Re: [gmx-users] analysis of different groups with g_energy

On Monday 09 June 2008 16:19, Justin A. Lemkul wrote: Well, ofcourse I did! otherwise I wouldn't expect any program to know them by itself! the problem is that I say: # g_energy -f ../ener.edr -s ../25ns.tpr -b 23000 -e 25000 -skip 25 -o tot_ener and I get: Opened ../ener.edr as single preci

Re: [gmx-users] analysis of different groups with g_energy

Choose appropriate energygrps in your .mdp file. -Justin Peyman Yamin wrote: Dear Gromacs users, I'm simulating dilute solutions of different surfactants in different media. All I want to analyse afterwards, though, is the single surfactant molecule properties! Is there any way to extract

[gmx-users] analysis of different groups with g_energy

Dear Gromacs users, I'm simulating dilute solutions of different surfactants in different media. All I want to analyse afterwards, though, is the single surfactant molecule properties! Is there any way to extract energy data from the original .edr file with respect to a single group, in the s

Re: Re: [gmx-users] Re:Time evolution of lipidbilayer

Thanks for your prompt reply, Yes I will do further analysis a)thickness of bilayer b) g_order of popc by using 5ns trjectory file. Thank you On Mon, 09 Jun 2008 Justin A.Lemkul wrote : >trjcat, then do your analysis. > >-Justin > >minnale wrote: >>Content-type: multipart/alternative; >>

Re: [gmx-users] Re:Time evolution of lipidbilayer

trjcat, then do your analysis. -Justin minnale wrote: Content-type: multipart/alternative; boundary="Next_1213018572---0-202.137.237.238-31592" This is a multipart mime message --Next_1213018572---0-202.137.237.238-31592 Content-type: text/plain; charset=iso-8859-1 Content-T

[gmx-users] Re:Time evolution of lipidbilayer

Content-type: multipart/alternative; boundary="Next_1213018572---0-202.137.237.238-31592" This is a multipart mime message --Next_1213018572---0-202.137.237.238-31592 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: in

Re: [gmx-users] extract conformations !!

Hi, On Monday, 9. June 2008 13:34, Anamika Awasthi wrote: > Dear Friends, >I want to extract conformations of each 1 ns from my 10 ns > simulation. >My this job is running for 20 ns, so shall I first stop my job and > then do this? >I tried this command without stopping my

Re: [gmx-users] Time evolution of lipidbilayer

minnale wrote: Hi all, This may be a trivial question I want to calculate "time evolution of area per lipid" The steps I have done are 1. Extracted BoxX and BoxY values of 5ns_popc.edr by using g_energy command. 2. I have written code for calculating area per lipid in way that boxX

Re: [gmx-users] extract conformations !!

Anamika Awasthi wrote: Dear Friends, I want to extract conformations of each 1 ns from my 10 ns simulation. My this job is running for 20 ns, so shall I first stop my job and then do this? I tried this command without stopping my job trjconv -f *.trr -o *.pdb -s

[gmx-users] extract conformations !!

Dear Friends, I want to extract conformations of each 1 ns from my 10 ns simulation. My this job is running for 20 ns, so shall I first stop my job and then do this? I tried this command without stopping my job trjconv -f *.trr -o *.pdb -s *.tpr -b -0 -e -10 -dump -1000

[gmx-users] Time evolution of lipidbilayer

Hi all, This may be a trivial question I want to calculate "time evolution of area per lipid" The steps I have done are 1. Extracted BoxX and BoxY values of 5ns_popc.edr by using g_energy command. 2. I have written code for calculating area per lipid in way that boxX multiply with box