[gmx-users] g_covar

2010-08-30 Thread Carla Jamous
Hi everyone, please I'm using gromacs 4.0.3, and I want to see the program g_covar, except that I have it in binary file and I want to see the C program in text format. Please how can I have access to it? Thank you Carla -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.or

Re: [gmx-users] g_covar

2010-08-30 Thread Justin A. Lemkul
Carla Jamous wrote: Hi everyone, please I'm using gromacs 4.0.3, and I want to see the program g_covar, except that I have it in binary file and I want to see the C program in text format. Please how can I have access to it? Download the source code, then look at src/tools/gmx_covar.c.

RE: [gmx-users] g_covar

2010-08-30 Thread #ZHAO LINA#
YourSourceCode/gromacs/src/tools/ If in Linux OS, try locate g_covar.c p.s 4.0.3 is not the latest version. why do not try the latest version? From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Carla Jamous [carlajam...@gmail.co

Re: [gmx-users] Re: NPT simulation

2010-08-30 Thread ms
On 30/08/10 01:19, Justin A. Lemkul wrote: Is it wrong? No, exactly as I have explained in the follow-up message to this post. I was trying to tie this concept into the OP's original observations and attempts to quantify his results with respect to energetics of individual molecules. Thanks

Re: [gmx-users] AFM Pulling Simulations

2010-08-30 Thread ms
On 26/08/10 19:56, chris.ne...@utoronto.ca wrote: Natalie: It would also be a good idea for you to ensure that your supervisor knows how difficult it is to learn and correctly apply these methods. If they think that a person can learn linux and gromacs and the gromacs pull code in a short period

Re: [gmx-users] LJ potential

2010-08-30 Thread Sai Pooja
Thanks Mark. I have just 2 more queries regarding this. *When using tables for the potential, * 1) For VdW interactions, it it alright to use the topology file generated by pdb2gmx using a forcefield (eg. CHARMM27) which specifies LJ paramters as 'sigma' and 'epsilon' instead of C6 and C12 as in

[gmx-users] Re: Re: Flat energy profile in g_wha

2010-08-30 Thread alexander yakovenko
Sorry for poor explanations. My histogram is here http://picasawe b.google.ca/117 558205101329348 732/G_wham#5511 244561053627250 it was 12 ns per window run. Regards, Alex.   alexander yakovenko wrote: > Hi Justin! > Thank you for replay. My histogram (can send if require

Re: [gmx-users] Re: Re: Flat energy profile in g_wha

2010-08-30 Thread Justin A. Lemkul
alexander yakovenko wrote: Sorry for poor explanations. My histogram is here http://picasawe b.google.ca/117 558205101329348 732/G_wham#5511 244561053627250 it was 12 ns per window run. Looks to me like your wi

[gmx-users] VDWradii.dat

2010-08-30 Thread nishap . patel
Hello, I have a question about how gromacs assigns VDW radii for ions. I checked the vdwradii.dat file but it does not mention any ions, so where do the parameters for ions come from? I got the .pqr file for sodium and I got the atomic radii of 1.6652A, I am not sure where that value c

Re: [gmx-users] VDWradii.dat

2010-08-30 Thread Justin A. Lemkul
nishap.pa...@utoronto.ca wrote: Hello, I have a question about how gromacs assigns VDW radii for ions. I checked the vdwradii.dat file but it does not mention any ions, so where do the parameters for ions come from? I got the .pqr file for sodium and I got the atomic radii of 1.6652A, I

Re: [gmx-users] VDWradii.dat

2010-08-30 Thread David van der Spoel
On 2010-08-30 20.32, nishap.pa...@utoronto.ca wrote: Hello, I have a question about how gromacs assigns VDW radii for ions. I checked the vdwradii.dat file but it does not mention any ions, so where do the parameters for ions come from? I got the .pqr file for sodium and I got the atomic radii o

[gmx-users] Re: NPT simulation

2010-08-30 Thread Vitaly Chaban
> System size is 5 *5*3 nm when density reaches around 600 SI. Can you please > explain what do you mean by "What about dependence heat of evaporation vs > system size ?". I dont know how to compute vap. heat in gromacs! 1. Just use g_energy and compute potential energy. Then proceed by definition

Re: [gmx-users] VDWradii.dat

2010-08-30 Thread nishap . patel
I did use this command: editconf -f md.tpr -mead na.pqr. If I understand it correctly for -sig56 option, I would use the min rvdw from my mdp and divide it by 2 and use that value in the command line? Quoting David van der Spoel : On 2010-08-30 20.32, nishap.pa...@utoronto.ca wrote: Hell

Re: [gmx-users] VDWradii.dat

2010-08-30 Thread nishap . patel
Also, I am using OPLS-AA force field with TIP3P water Quoting David van der Spoel : On 2010-08-30 20.32, nishap.pa...@utoronto.ca wrote: Hello, I have a question about how gromacs assigns VDW radii for ions. I checked the vdwradii.dat file but it does not mention any ions, so where do the par

[gmx-users] Flat energy profile in g_wham

2010-08-30 Thread chris . neale
Alexander: Can you please also post your free energy profile out of wham? Also, can you confirm that you are using different force constants for different windows? Justin is correct, but that just means that you are using more cpus than you need... it's not actually wrong. What are your u

Re: [gmx-users] VDWradii.dat

2010-08-30 Thread Justin A. Lemkul
nishap.pa...@utoronto.ca wrote: I did use this command: editconf -f md.tpr -mead na.pqr. If I understand it correctly for -sig56 option, I would use the min rvdw from my mdp and divide it by 2 and use that value in the command line? The value of rvdw is taken from the -rvdw flag, per the d

Re: [gmx-users] VDWradii.dat

2010-08-30 Thread nishap . patel
Okay I see what you mean. Thanks alot! Quoting "Justin A. Lemkul" : nishap.pa...@utoronto.ca wrote: I did use this command: editconf -f md.tpr -mead na.pqr. If I understand it correctly for -sig56 option, I would use the min rvdw from my mdp and divide it by 2 and use that value in th

[gmx-users] Re: Re: Re: Flat energy profile in g_wham

2010-08-30 Thread alexander yakovenko
I don't know in advance which of them are redundant; moreover I am surprised if better scan of configuration space is something weird. Anyway I removed some windows (see histograms here http://picasaweb.google.ca/117558205101329348732/G_wham#5511287294315721970) and now PMF profile is 0.00e

[gmx-users] Flat energy profile in g_wham

2010-08-30 Thread chris . neale
Alexander, please post the following: 1. force constants for your plot at http://picasaweb.google.ca/117558205101329348732/G_wham#5511287294315721970 NOTE: if they are all 1000 as in your first post, then you have a problem in your sampling. 2. units for your x-axis in the plot mentioned

[gmx-users] Tables with forcefield

2010-08-30 Thread Sai Pooja
Hi, When using tables for the potential, 1) For VdW interactions, it it alright to use the topology file generated by pdb2gmx using a forcefield (eg. CHARMM27) which specifies LJ paramters as 'sigma' and 'epsilon' instead of C6 and C12 as in the case of user defined potentials? I ask this becaus

[gmx-users] Re: Re: Re: Re: Flat energy profile in g_wham

2010-08-30 Thread alexander yakovenko
0. Thank you all who spent time answering my post (and especially for explanations how to convert bins into energy)! 1. Yes, force is 1000 kJ/mol/nm^2 in all windows 2. z is in nm as default in wham 3. I made profile for w#10 (just in the case I attach forces file). the picture of window pr

Re: [gmx-users] LJ potential

2010-08-30 Thread Mark Abraham
- Original Message - From: Sai Pooja Date: Tuesday, August 31, 2010 2:45 Subject: Re: [gmx-users] LJ potential To: Discussion list for GROMACS users > > Thanks Mark. I have just 2 more queries regarding this. > > When using > tables for the potential, > > 1) For VdW interactions

[gmx-users] Re: Re[5]: Flat energy profile in g_wham

2010-08-30 Thread chris . neale
First, I don't think that you converted and debiased correctly. Once you have a histogram of the displacement, then you will debias that histogram like this (assuming run at 298K): FC=1000 T=298 cat biased.hist |awk '{print $1,-0.00831447*'${T}'*log($2)-0.5*'${FC}'*$1*$1}' > debiased.hist

[gmx-users] Distance from heavy atom to Methyl Vsite

2010-08-30 Thread Roland Schulz
Hi, how does one calculate the distance from the next heavy atom to the MCH3 virtual site of a methyl group? I have a O-C-H3 and thus need to parameterize the constraint length for MCH3 to the oxygen. I can't find or figure out the formula to compute this. Roland -- ORNL/UT Center for Molecular

[gmx-users] Re: Re[7]: Flat energy profile in g_wham

2010-08-30 Thread chris . neale
First, you confuse me when you say "pulling direction was along Y-axis" since your .mdp file indicates pull_dim = Y Y Y and so you are pulling in *all* dimensions. Your profile doesn't look like mine at all, but then again I took mine from a force profile. Now that I can see your forces and

[gmx-users] Re: Re[7]: Flat energy profile in g_wham

2010-08-30 Thread alexander yakovenko
Sorry for mixing things, I do pull into N Y N direction and then performed umbrella simulation at Y Y Y for each distances window. This is very good question, actually I don't realize it too. The only thing what I can say is that I haven't edited/renamed these files, just copy them. S

[gmx-users] Re: Re[7]: Flat energy profile in g_wham

2010-08-30 Thread chris . neale
So now we have the first real lead. Next is for you to simplify your system to the point where you *can* understand the relationship between the pullf and pullx files. For example, I always suggest a water bath of explicit water with the sd integrator and apply the pull code to two waters.

[gmx-users] g_hbond

2010-08-30 Thread Nilesh Dhumal
Hello, I have a system with a glucose molecule and 256 water molecules. I want to find out the number of hydrogen bond between the hydrogen atom of OH group of glucose and the oxygen atom of water. How can I make the index file. Thanks NIlesh -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] g_hbond

2010-08-30 Thread Justin A. Lemkul
Nilesh Dhumal wrote: Hello, I have a system with a glucose molecule and 256 water molecules. I want to find out the number of hydrogen bond between the hydrogen atom of OH group of glucose and the oxygen atom of water. How can I make the index file. Type "help" at the make_ndx prompt for exa

Re: [gmx-users] g_hbond

2010-08-30 Thread Mark Abraham
- Original Message - From: Nilesh Dhumal Date: Tuesday, August 31, 2010 12:42 Subject: [gmx-users] g_hbond To: gmx-users@gromacs.org > Hello, > I have a system with a glucose molecule and 256 water molecules. > I want to find out the number of hydrogen bond between the > hydrogen atom

[gmx-users] Re: Re[7]: Flat energy profile in g_wham

2010-08-30 Thread alexander yakovenko
It is 2 options why I can’t understand relation between pullf and pullx: either I have no imagine how they should related or they related so that one can’t even imagine (say due to bug or file format). Till now my view was that we need a force to keep two molecules at asked separation. The fo

Re: [gmx-users] g_hbond

2010-08-30 Thread Nilesh Dhumal
THanks. I have one more system dioxin + water molecules. There is possiblity of C-H---O hydrogen bond. The CH bond of dioxin and oxygen atom of water. I want to calculate the number of hydrogen bonds. I used the following command g_hbond -f dix-bdmp.trr -s dix-bdmp.tpr -n dix-bdmp-no.ndx -num I