[gmx-users] about g_sas analysis

Dear gromacs users, I have some doubts regarding the options to be selected in g_sas program. g_sas asks for two groups, first one for calculation and second one for output. As I have understood from the manual that first group should contain all non solvent groups and second one the whole or part

Re: [gmx-users] about g_sas analysis

supti mukherjee wrote: Dear gromacs users, I have some doubts regarding the options to be selected in g_sas program. g_sas asks for two groups, first one for calculation and second one for output. As I have understood from the manual that first group should contain all non solvent groups and s

Re: [gmx-users] about g_sas analysis

Hi, Recently there was a relatively extensive discussion on the list regarding g_sas. Check the archives. Cheers, Tsjerk On Thu, Mar 18, 2010 at 9:07 AM, Milan Melichercik wrote: > supti mukherjee wrote: >> >> Dear gromacs users, >> I have some doubts regarding the options to be selected in g_

[gmx-users] query regarding normal mode analysis

hi, I am trying to do a normal mode analysis on a protein.I tried to energy minimize the structure, but was not being able to bring the Fmax less than that of the order 1.0e-03. Then I used the following ".mdp" file where I used the l-bfgs minimization method, using "cut-off

[gmx-users] query regarding normal mode analysis

hi, I am trying to do a normal mode analysis on a protein.I tried to energy minimize the structure, but was not being able to bring the Fmax less than that of the order 1.0e-03. Then I used the following ".mdp" file where I used the l-bfgs minimization method, using "cut-off

[gmx-users] Re: script to constraint distance between ligand and protein

Hi, I don't have a version of this tool that I'm comfortable distributing at this point (for what it's worth, the message you're referring to is almost 4 years old!). You should be able to get help with your specific topology file problem on-list. Free energy calculations are one of the har

[gmx-users] Re: g_desort

Dear Jennifer: I have tried to download the package to reproduce your problem, but have been unable. http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software links to G_DESORT.tgz, but that link sends me to: http://www.gromacs.org/@api/deki/files/54

[gmx-users] charge group assignment with AMBER parameters

I am attempting a simulation of a drug molecule using the ffamber/gaff within gromacs. When it comes to assigning charge groups the manual says that one should group together nearby atoms and the groups should have a net integer charge. Since AMBER charge parameters are obtained from QM calcu

[gmx-users] g_covar -ref

Hi Has anyone studied the effect of using different reference structures, not the average structure, when carrying out PCA. Does it make sense to use a structure besides the average to calculate the covariance matrix? Thanks Vijaya ___

[gmx-users] g_covar -ref

Hi Does anyone studied the effect of using different reference structures, not the average structure, when carrying out PCA. Does it make sense to use a structure besides the average to calculate the covariance matrix? Thanks Vijaya __

Re: [gmx-users] charge group assignment with AMBER parameters

Jacob Spooner wrote: I am attempting a simulation of a drug molecule using the ffamber/gaff within gromacs. When it comes to assigning charge groups the manual says that one should group together nearby atoms and the groups should have a net integer charge. Since AMBER charge parameters are

Re: [gmx-users] g_covar -ref

Hi Vijaya, Well, to start with that will be something as calculating the 'fluctuation' as sum((xi-ri)^2)/N, with xi and ri denoting the ith atom of the conformation x and the reference structure r and the sum is over time/observations. In the case of no variation in xi, the value you get will stil

RE: [gmx-users] g_covar -ref

PCA refers to covariance analysis (though SVD gives the same results). Principal components are obtained by projecting the trajectory onto the eigenvectors of the covariance matrix. I just wanted to know why the option -ref was offered and if it had any significance. Thanks Vijaya > Date: Thu,

Re: [gmx-users] g_covar -ref

Hi Vijaya, I'm sorry if I didn't quite get that first sentence of yours. Did you meant to start it with "I thought that ..."? Or were you trying to explain me something you thought I missed? PCA stands for 'principal component analysis', not 'covariance analysis'. For instance, PCA can be applied

RE: [gmx-users] g_covar -ref

Hi Your answer truly eludes me, unless -ref is an useless option. In any case it isn't particularly important. Vijaya > Date: Thu, 18 Mar 2010 19:37:40 +0100 > Subject: Re: [gmx-users] g_covar -ref > From: tsje...@gmail.com > To: gmx-users@gromacs.org > > Hi Vijaya, > > I'm sorry if I didn't

[gmx-users] What is Dmax, and are .tpr files transferrable between operating systems

Can someone tell me what the Dmax value is that is output to the terminal during energy minimization? Example output: Step= 2164, Dmax= 6.2e-03 nm, Epot= -1.17364e+06 Fmax= 8.49209e+02, atom= 56 Step= 2165, Dmax= 7.5e-03 nm, Epot= -1.17365e+06 Fmax= 1.05171e+04, atom= 56 Step= 2166, Dmax=

Re: [gmx-users] What is Dmax, and are .tpr files transferrable between operating systems

Warren Gallin wrote: Can someone tell me what the Dmax value is that is output to the terminal during energy minimization? Dmax is the largest step size taken. Example output: Step= 2164, Dmax= 6.2e-03 nm, Epot= -1.17364e+06 Fmax= 8.49209e+02, atom= 56 Step= 2165, Dmax= 7.5e-03 nm, Epot=

Re: [gmx-users] g_covar -ref

Hi Vijaya, > Your answer truly eludes me, unless -ref is an useless option. Well, that's pretty close to the conclusion. The use is limited to a few very specific cases and it might be better to hide the option from the view of casual users. But apparently you didn't catch the why yet. If you im

RE: [gmx-users] g_covar -ref

Hi Thanks for your input, what are the few specific cases where a reference structure might be used? Vijaya > Date: Thu, 18 Mar 2010 20:42:36 +0100 > Subject: Re: [gmx-users] g_covar -ref > From: tsje...@gmail.com > To: gmx-users@gromacs.org > > Hi Vijaya, > > > Your answer truly eludes me, un

Re: [gmx-users] g_covar -ref

Hi Vijaya, Hmmm. Well, it may make some sense to take a defined extreme point to take deviations from. Like for motion on an arc, it may make sense to take the center of the circle to determine the deviations. But what that will yield; how that translates to wiggling proteins... :S Cheers, Tsjer

[gmx-users] T-coupling groups

Dear GROMACS users, I have checked the mails in archive which deal with the problem I am facing but did not find the answer what I do wrong. I want to compile a PEO chain centered in box of 2900 water molecules. In my md.mdp the relevant section is as follows Tcoupl  =  nose-hoover

Re: [gmx-users] T-coupling groups

Zuzana Benkova wrote: Dear GROMACS users, I have checked the mails in archive which deal with the problem I am facing but did not find the answer what I do wrong. I want to compile a PEO chain centered in box of 2900 water molecules. In my md.mdp the relevant section is as follows Tcoupl

Re: [gmx-users] T-coupling groups

Dear Zuzana, Recently i have done similar selection, I have got this error only when i miss some atoms or when i have some atoms in both groups. I would suggest you to check your groups carefully or you can make indexes for these selections in VMD and check whether you are missing some atoms from

[gmx-users] g_bundle problem

I have tried using g_bundle in order to analyse helix axes in my transmembran helices. I created two groups in my ndx file that included the alpha carbons of the first half of my helix and a second group for the alpha carbons for the second half. When I try using g_bundle the following error comes

Re: [gmx-users] g_bundle problem

Stefan Hoorman wrote: I have tried using g_bundle in order to analyse helix axes in my transmembran helices. I created two groups in my ndx file that included the alpha carbons of the first half of my helix and a second group for the alpha carbons for the second half. When I try using g_bundl

Re: [gmx-users] g_bundle problem

Justin A. Lemkul wrote: Stefan Hoorman wrote: I have tried using g_bundle in order to analyse helix axes in my transmembran helices. I created two groups in my ndx file that included the alpha carbons of the first half of my helix and a second group for the alpha carbons for the second hal

Re: [gmx-users] g_bundle problem

On Friday 19 March 2010 02:36:49 Stefan Hoorman wrote: > I have tried using g_bundle in order to analyse helix axes in my > transmembran helices. I created two groups in my ndx file that included the > alpha carbons of the first half of my helix and a second group for the > alpha carbons for the s

[gmx-users] removal of center of mass motion needed for accelerated water molecules?

Hi all, I have a periodical system comprised a nanotube and water solvent. Positive acceleration is applied to every water molecules and I am trying to count the water flux through the nanotube. I also specified force constraints (1000) on the nanotube to keep it in place. The question is whether

[gmx-users] compile problem on Centos X86_64 with gcc44 and fftw2

Title: compile problem on Centos X86_64 with gcc44 and fftw2 Dear all users, I compiled the program likes this: a, fftw3   ./configure --enable-float make   make install. All sounds ok b, gromacs4.0.5   ./configure --with-fft=fftw3  make make install. All sound ok. However when I copy gmxt

Re: [gmx-users] compile problem on Centos X86_64 with gcc44 and fftw2

Wu Rongqin wrote: Dear all users, I compiled the program likes this: a, fftw3 ./configure --enable-float make make install. All sounds ok b, gromacs4.0.5 ./configure --with-fft=fftw3 make make install. All sound ok. Why not install the latest version (4.0.7)? You'll get the latest

答复: [gmx-users] compile problem on Cen tos X86_64 with gcc44 and fftw2

Title: ´ð¸´: [gmx-users] compile problem on Centos X86_64 with gcc44 and fftw2 Dear Dr. Justin, I also followed your tutorial "Lysozyme in Water" on website. However, on the energy miminization step, I cannot reproduce your results. The minimization stopped at 61 steps. However, Sometimes it

Re: 答复: [gmx-users] compile probl em on Centos X86_64 with gcc44 and fftw2

- Original Message - From: Wu Rongqin Date: Friday, March 19, 2010 16:10 Subject: 答复: [gmx-users] compile problem on Centos X86_64 with gcc44 and fftw2 To: jalem...@vt.edu, Discussion list for GROMACS users , Discussion list for GROMACS users > ´ð¸´: [gmx-users] compile problem