[gmx-users] g_rotacf error

Hello gromacs users, I´m currently tring to calculate S2 order parameters for comparison with nmr data and other simulations. When i try the command for the NH vector: g_rotacf -s ../protein.tpr -d -P 2 -n nh.ndx -f ../protein_fit.xtc -w -noaver It gives me the only half of the residues (NH

Re: [gmx-users] g_rotacf error

On 10/29/13 4:02 PM, Tiago Gomes wrote: Hello gromacs users, I´m currently tring to calculate S2 order parameters for comparison with nmr data and other simulations. When i try the command for the NH vector: g_rotacf -s ../protein.tpr -d -P 2 -n nh.ndx -f ../protein_fit.xtc -w -noaver It

[gmx-users] g_rotacf autocorrelation function

Hi, I am trying to locate code for angle auto-correlation function (ACF) in GROMACS 4.0.7. Angle ACF is calculated by g_rotacf for GROMACS (gmx_rotacf.c). In line 194 of gmx_rotacf.c, it calls do_autocorr. This function is in gstat.h file line 125 - 185. But I don't see any actual code which

[gmx-users] g_rotacf

Hi, I have tried to use g_rotacf to get the rotational autocorrelation plot for a n-h vector, and I have two questions: 1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why? 2. The plot is bottom out at 500 ps and then go back up. What does it mean physically? Thanks for your insight.

Re: [gmx-users] g_rotacf

On 4/06/2011 9:02 AM, simon sham wrote: Hi, I have tried to use g_rotacf to get the rotational autocorrelation plot for a n-h vector, and I have two questions: 1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why? This can be normal for computed correlation functions. See chapter

Re: [gmx-users] g_rotacf

On 4/06/2011 11:27 AM, Mark Abraham wrote: On 4/06/2011 9:02 AM, simon sham wrote: Hi, I have tried to use g_rotacf to get the rotational autocorrelation plot for a n-h vector, and I have two questions: 1. My MD run is 20ns, but the rotacf.xvg shows only 10ns. why? This can be normal for

[gmx-users] g_rotacf NH vector relaxation

Dear gromacs users, I want to calculate NH vector for my ligand simulations using g_rotacf. I want to ask if I first need to remove rotation and translation degrees of freedom from the trajectory using the command: trjconv -f traj.xtc -s 10nsProd_MD.tpr -fit rot+trans -o no_rot_trans.xtc Also,

[gmx-users] g_rotacf create tpr from pdb

Dear Gromacs experts and newbies, The program g_rotacf (calculates the autocorrelation function) requires as input for the -s option either a tpr, tpb or tpa file. I does not accept for the -s option a PDB file :- ( . How can I create from a pdb file a tpr file? The program pdb2gmx can only

[gmx-users] g_rotacf create tpr from pdb

Der Gromacs users and dear Justin, The gromacs tutorial does not really tell how to create a tpr without a mdp file. The standard procedure in the tutorials is to use the program grompp which always requires a mdp file. But for calculating the autocorrelation function I only need the coordinates

Re: [gmx-users] g_rotacf create tpr from pdb

henri mone wrote: Der Gromacs users and dear Justin, The gromacs tutorial does not really tell how to create a tpr without a mdp file. The standard procedure in the tutorials is to use the program grompp which always requires a mdp file. But for calculating the autocorrelation function I only

Re: [gmx-users] g_rotacf, order parameter S2 problem

On Sun, 11 Jan 2009 12:50:00 +0800 Dechang Li li.d...@gmail.com wrote: Dear all, I used g_rotacf to calculate the order parameter (S2, N-H bond in main chian). Thanks to Xavier Periole's advice, I make the index file and obtained some results. However, some results I got made me puzzling

RE: [gmx-users] g_rotacf, order parameter S2 problem

Hi, I would say rotational acf's can be negative. In most cases this will indicate bad sampling. This is not suprising considering the extremely long times you printed. I guess you get positive values for shorter correlation times. Berk From: x.peri...@rug.nl Subject: Re: [gmx-users

Re: [gmx-users] g_rotacf, order parameter S2 problem

Dechang Li wrote: Dear all, I used g_rotacf to calculate the order parameter (S2, N-H bond in main chian). Thanks to Xavier Periole's advice, I make the index file and obtained some results. However, some results I got made me puzzling that the order parameter is negative! Here is

[gmx-users] g_rotacf, order parameter S2 problem

Dear all, I used g_rotacf to calculate the order parameter (S2, N-H bond in main chian). Thanks to Xavier Periole's advice, I make the index file and obtained some results. However, some results I got made me puzzling that the order parameter is negative! Here is one of my results: @

Re: [gmx-users] g_rotacf

Daniel K wrote: How should I change it so it calculates the 40 ps? You need at least a 80ps trajectory otherwise you basically have too less data to correlate with with a lag time of 40ps. Check gromacs manual 4.0 at section 8.5 On Wed, Oct 22, 2008 at 6:34 PM, Xavier Periole [EMAIL

[gmx-users] g_rotacf

I have been trying to use g_rotacf with a simulation run for 40 ps (2) with steps of 2fs and the frames where extracted every 50 fs (25 frames). The trajectory file is correct because it has 801 frames. When I calculate the g_rotacf I only get 20 ps and the time step is 50 fs. Does any body no

Re: [gmx-users] g_rotacf

On Wed, 22 Oct 2008 17:38:58 -0400 Daniel K [EMAIL PROTECTED] wrote: I have been trying to use g_rotacf with a simulation run for 40 ps (2) with steps of 2fs and the frames where extracted every 50 fs (25 frames). The trajectory file is correct because it has 801 frames. When I calculate

Re: [gmx-users] g_rotacf

How should I change it so it calculates the 40 ps? On Wed, Oct 22, 2008 at 6:34 PM, Xavier Periole [EMAIL PROTECTED] wrote: On Wed, 22 Oct 2008 17:38:58 -0400 Daniel K [EMAIL PROTECTED] wrote: I have been trying to use g_rotacf with a simulation run for 40 ps (2) with steps of 2fs and

[gmx-users] g_rotacf -normalize

Dear users, The default -normalize option in g_rotacf is set to yes. Does it mean that the vector of interest is always be a unit vector ? If so, this has to be set to -nonormalize I suppose if one is interested about the internal dynamics of a system. Please let me know whether I am correct or

Re: [gmx-users] g_rotacf

On Thu, 4 Sep 2008 21:13:39 -0400 rams rams [EMAIL PROTECTED] wrote: Hi Xavier, I have a question about the accuracy of the correlation times obtained using gromacs tools. (I am getting these by integrating the output .xvg file of g_rotacf using g_analyze). Since the experimental values are

Re: [gmx-users] g_rotacf

One thing I totally forgot to mention is that you can not access the overall rotational motion of the protein using the NH vectors! These would contain both internal and overall motion. Have a look at papers from Lipari and Szabo JACS-1982 for the initial model and from Bruschweiler Current

Re: [gmx-users] g_rotacf

Dear Xavier, Thank you very much for your valuable inputs. I am extremely sorry for troubling you quite often. You are absolutely right and I am using the second order legendre polynomials to obtain the correlation function only (am not using this to fit the correlation function data). The

Re: [gmx-users] g_rotacf

On Wed, 3 Sep 2008 23:40:14 -0400 rams rams [EMAIL PROTECTED] wrote: Hi, I am so surprised for not finding any one who have better experience with g_rotacf. I have been playing around with it and the time correlation value I got by g_rotacf is so small in comparison to the time correlation

Re: [gmx-users] g_rotacf

Hi Xavier, I am extremely sorry for incomplete information. But this is a follow up to my previous two emails. Unfortunately I havent received any suggestions for them and it appears like you too missed them. For more clarity I am pasting them here again: Dear users, To calculate the

Re: [gmx-users] g_rotacf

On Thu, 4 Sep 2008 09:45:34 -0400 rams rams [EMAIL PROTECTED] wrote: Hi Xavier, I am extremely sorry for incomplete information. But this is a follow up to my previous two emails. Unfortunately I havent received any suggestions for them and it appears like you too missed them. For more clarity

Re: [gmx-users] g_rotacf

Hi Xavier, I have a question about the accuracy of the correlation times obtained using gromacs tools. (I am getting these by integrating the output .xvg file of g_rotacf using g_analyze). Since the experimental values are not available to compare, I am not so sure about the correlation times I

[gmx-users] g_rotacf

Hi, I am so surprised for not finding any one who have better experience with g_rotacf. I have been playing around with it and the time correlation value I got by g_rotacf is so small in comparison to the time correlation value I calcualted using the hydrodynamic radius of the protein. The value

[gmx-users] g_rotacf

Dear users, To calculate the rotational auto correlation functions, the command mentioned in the maual is: g_rotacf -P 1 -nparm 2 -fft -n index -o .xvg -fa -beginfit -endfit what are the -nparm and -fa options are meant for ? Also do we need to use -fitfn option to obtain the rotational auto

[gmx-users] g_rotacf

Dear users, I have given a command like the following to calculate the rotational auto correlation function: g_rotacf -f .trr -s .tpr -P 2 -fft -o .xvg -b -e 1 -n .ndx -d I want to use the second order Legendre polynomial to fit. I integrated the resulting .xvg file, to obtain the

[gmx-users] g_rotacf

Hi, I want to clarify a few of the things about the usage of g_rotacf (for rotational correlation function for molecules). In the manual it is given like the following: g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1 -beginfit 2.5 -endfit 20.0 I understood that -f, -s

[gmx-users] g_rotacf

Dear All I have what might be a simple question. For g_rotacf, what is the equation used in the calculation of the rotational correlation function? is there any basic reference one could give me for the same? Also, for the rotational correlation function, is the decay something as simple as the

Re: [gmx-users] g_rotacf

Rama Gullapalli wrote: Dear All I have what might be a simple question. For g_rotacf, what is the equation used in the calculation of the rotational correlation function? is there any basic reference one could give me for the same? Also, for the rotational correlation function, is the decay

Re: [gmx-users] g_rotacf again

Hi Rama, You would be able to do it by taking one of two approaches: 1. Write the centers of masses and from this generate a multipdb file (or gro file) containing three atoms spanning two vectors perpendicular to the vector between these centers of masses. This trajectory can be used for

[gmx-users] g_rotacf again

Hello everybody.I have question regarding g_rotacfIf I wanted to compute the rotational correlation function of a linear vector which is between the "centers of masses" of two groups of atoms in an individual molecule (Instead of two atoms), how do I go about it?Can I use g_rotacf to do it ?Thanks

Re: [gmx-users] g_rotacf

Dear Dr SpoelThank you for the reply. But I do not quite follow how -noaver does it. I want to compute the P-N vector of lipid molecules and average it over the 128 molecules in the bilayer.Do I make a group containing the numbers of the P and N molecules in a single group ( 256 atoms) and use

Re: [gmx-users] g_rotacf

Dear Dr Spoel Sorry for the earlier hasty mail. I figured out how the -noaver option works. Thanks Sincerely Regards RamaRama Gullapalli [EMAIL PROTECTED] wrote: Dear Dr SpoelThank you for the reply. But I do not quite follow how -noaver does it. I want to compute the P-N vector of lipid

[gmx-users] g_rotacf

Hello everybody,I have nearly 100 different vectors to analyse using g_rotacf. I was wondering if there was anyway to do this in GROMACS simultaneously since g_rotacf does not have have the -ng option like in g_traj or others.I would imagine one could use a awk script to run g_rotacf to