Re: [gmx-users] Pressure Fluctuations

On 16/03/11, Kavyashree M hmkv...@gmail.com wrote: Dear users, Upon was trying to simulate an npt ensemble (protein in water), pressure was coupled using  parinello rahman system with tau_p = 2, tau_t = 1; compressibility 4.5e-5, type = isotropic. (cut off scheme (vdw_type = switch;

Re: [gmx-users] Re: g_hbond output

If I understand correctly, $2 is the number of hydrogen bonds defined by cutoff distance and the cutoff angle. $3 is the number of pairs within the cutoff distance, but beyond the cutoff angle. You may got different number of hbonds using different cutoff distance and cutoff angle. Jianguo

Re: [gmx-users] Re: g_hbond output

s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2 1000 1 0 Here is my question, since

Re: [gmx-users] Energy calculation

Hi, I try to calculate the Hbond in the ligand and remove the duplicate atoms in the .ndx file dumped from g_hbond. This is the contents in the .ndx file. [ HBD ] 17385 17382 17422 17419 17459 17456 17496 17493 17533 17530 [ HBA ] 17367 17375 17381 17384 17387 17388 17400 17404 17412

Re: [gmx-users] Energy calculation

On 16/03/11, C.Y. Chang chiayun.ch...@gmail.com wrote: Hi, I try to calculate the Hbond in the ligand and remove the duplicate atoms in the .ndx file dumped from g_hbond. This is the contents in the .ndx file. [ HBD ]  17385 17382 17422 17419 17459 17456 17496 17493 17533 17530 [

[gmx-users] Re: gmx-users Digest, Vol 83, Issue 106

Thank you Angel, I will try your suggestion. Cheers SA Hi very recently I faced the same problem with a system that gives micelles of different geometries and, as far as I saw, g_order don't do that. Then I decided to compute a kind of local order parameters defined as: S_i=(3

Re: [gmx-users] Re: gmx-users Digest, Vol 83, Issue 106

Then, please, let us know how it works for your systems. The results for my systems were exactly as expected. This allows to evaluate the order of the C-chains regardless their orientation... but I do not know if there is a better method to do this. I would be happy to know the opinion of anyone

Re: [gmx-users] Re: g_hbond output

A pair within the cutoff distance (e.g., 0.35nm) either belongs to $2 or $3, but cannot belong to both columns. If the program finds a pair shorter than 0.35nm, and the angle is smaller than 30deg., then the program put this pair in the column 2. If the program finds a pair shorter than

Re: [gmx-users] Pulling

Dear Chris Thanks for your reply 2-When you limit your sampling phase space,it can make some Errors,Because you may ignore some important regions(where you don't know them and you can't predict there). In the other hands,When we pull drug along a line,although we had not restrain it, but in fact

Re: [gmx-users] Umberella sampling

Dear chris Thanks for your reply 1-I am not sure,Since we need the know the variations of free energy along a specific degree of freedom of system(for example z axis),so the springs must be 1 dimensional to allow drug to oscilate only in one dimension(z axis). Let me say my question in other

[gmx-users] pdb2gmx 4.5.3 fails with free amino acid with amber99sb but runs fine with opls-aa BUG ?

Hello I am trying to pdb2gmx with a free amino acid in amber99sb as follows: pdb2gmx -f temp.pdb -ff amber99sb there are no ter records in the input pdb file. However, pdb2gmx fails with the following error: --- Program pdb2gmx, VERSION

Re: [gmx-users] pdb2gmx 4.5.3 fails with free amino acid with amber99sb but runs fine with opls-aa BUG ?

On 2011-03-16 11.29, maria goranovic wrote: Hello I am trying to pdb2gmx with a free amino acid in amber99sb as follows: pdb2gmx -f temp.pdb -ff amber99sb there are no ter records in the input pdb file. However, pdb2gmx fails with the following error:

[gmx-users] installation of gromacs

Hello, I did the procedure as described, but at the end of the configuration of gromacs, I obtain this message: checking size of void*... configure: error: cannot compute sizeof (void*) See `config.log' for more details. What is the problem? Regards, Thomas -- Empfehlen Sie GMX DSL Ihren

Re: [gmx-users] installation of gromacs

On 16/03/11, Thomas Koller koller-tho...@gmx.de wrote: Hello, I did the procedure as described, but at the end of the configuration of gromacs, I obtain this message: checking size of void*... configure: error: cannot compute sizeof (void*) See `config.log' for more details. What

[gmx-users] Fwd: membrane protein

-- Forwarded message -- From: mohsen ramezanpour ramezanpour.moh...@gmail.com Date: Wed, Mar 9, 2011 at 2:49 PM Subject: membrane protein To: Discussion list for GROMACS users gmx-users@gromacs.org Dear All in membrane protein tutorial: What is the P-N vector? RMSD for what

[gmx-users] Fwd: membrane-protein

-- Forwarded message -- From: mohsen ramezanpour ramezanpour.moh...@gmail.com Date: Tue, Mar 8, 2011 at 11:33 PM Subject: membrane-protein To: Discussion list for GROMACS users gmx-users@gromacs.org Dear All doing membrane protein tutorial of Dr.Justin I have a few question,

[gmx-users] Phd positions in SISSA

Dear all, since many people in our group are gromacs users, this announcement could make some sense on the gmx mailing list. Please forward it to interested people. Best wishes, Giovanni Bussi # Job Description: Applicants should have a good background in Physics, Chemistry or related

[gmx-users] g_order for DPC alkyl chain in the micelle

Hi all This message is related with my previous message (see below) about the calculation of the order value for the DPC alkyl chain in a micelle. So if I understand well the previous angel's message, I need to compute the theta angle between the 2 vectors defined by the (i-1,i+1) and (i, i+2).

Re: [gmx-users] g_order for DPC alkyl chain in the micelle

sa wrote: Hi all This message is related with my previous message (see below) about the calculation of the order value for the DPC alkyl chain in a micelle. So if I understand well the previous angel's message, I need to compute the theta angle between the 2 vectors defined by the

Re: [gmx-users] Pressure Fluctuations

Thank you Sir I am using OPLSAA with tip4p water model, I agree to the fact that it will oscillate but the oscillation is this case was from appr. -1000bar to 1000bar. And as it is stated in the FAQ regarding the variation of fluctuations with number of waters, this system has 6882 waters

Re: [gmx-users] Pressure Fluctuations

Kavyashree M wrote: Thank you Sir I am using OPLSAA with tip4p water model, I agree to the fact that it will oscillate but the oscillation is this case was from appr. -1000bar to 1000bar. And as it is stated in the FAQ regarding the variation of fluctuations with number of waters, this

Re: [gmx-users] Re: g_hbond output

ZHAO Lina skrev 2011-03-16 06.33: @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 0 0 200 0 0 400 2 1 600 0 3 800 0 2

Re: [gmx-users] Re: g_hbond output

Erik Marklund skrev 2011-03-16 16.25: ZHAO Lina skrev 2011-03-16 06.33: @ legend length 2 @ s0 legend Hydrogen bonds @ s1 legend Pairs within 0.35 nm 0 0 0 200 0 0 400 2 1 600 0 3

Re: [gmx-users] g_order for DPC alkyl chain in the micelle

Dear SA To be honest I am not sure this can be done by using g_angle, I used my own code for this calculation. I could send it to you if you send me a message off the list... but I would prefer to talk with a non-anonymous. Cheers, Ángel. On Wed, 2011-03-16 at 15:58 +0100, sa wrote: Hi all

[gmx-users] Re: g_order for DPC alkyl chain in the micelle

Ok Justin, So which gmx tool i can use to obtain the angle between two vectors defined by two atom pairs ? SA sa wrote: Hi all This message is related with my previous message (see below) about the calculation of the order value for the DPC alkyl chain in a micelle. So if I

[gmx-users] Density of methanol too low

Dear list members, I am running some simple simulations of pure ethanol and methanol using the opls-aa force field as implemented in GROMACS 4.5.3, as a test case before attempting to study mixtures with more complex molecules. My problem is that, even though there are published results [1]

Re: [gmx-users] Density of methanol too low

On 2011-03-16 16.35, Jesús Carrete Montaña wrote: Dear list members, I am running some simple simulations of pure ethanol and methanol using the opls-aa force field as implemented in GROMACS 4.5.3, as a test case before attempting to study mixtures with more complex molecules. My problem is

Re: [gmx-users] Pressure Fluctuations

Thank you Justin, When I went through most of the mailing list the fluctuations are not so high and even in the FAQ it was mentioned in the range of 500-600 bar for 216 water. And more over the average pressure was ~6bar instead of 1bar which was required. So would you suggest that I can

[gmx-users] dipole moment autocorrelation function

Hello, I am trying to calculate the non normalized dipole moment autocorrelation function for water. I am using flexible spc water model (define=-DFLEX_SPC). I am using gromacs 4.0.7 version. I run the simulation for 200 ps. I run the following command to calculate the dipole moment

Re: [gmx-users] Re: g_order for DPC alkyl chain in the micelle

sa wrote: Ok Justin, So which gmx tool i can use to obtain the angle between two vectors defined by two atom pairs ? Well, that's what g_sgangle does. What I said was that if you have to do this more than a few times (since you have to do every pair of atoms separately), this can be

[gmx-users] Pulling

2-When you limit your sampling phase space,it can make some Errors, Because you may ignore some important regions(where you don't know them and you can't predict there). I agree with the idea that underlies your point, but it is not a problem. You don't need to sample all intervening phase

Re: [gmx-users] Pressure Fluctuations

Thank you Justin! On Wed, Mar 16, 2011 at 9:28 PM, Justin A. Lemkul jalem...@vt.edu wrote: Kavyashree M wrote: Thank you Justin, When I went through most of the mailing list the fluctuations are not so high and even in the FAQ it was mentioned in the range of 500-600 bar for 216

[gmx-users] Umberella sampling

Mohsen: To be honest, this just sounds like debating. I have offered you my perspective already. Chris. -- original message -- Dear chris Thanks for your reply 1-I am not sure,Since we need the know the variations of free energy along a specific degree of freedom of system(for example z

[gmx-users] Website search down again

Hi, Just a heads-up, the Gromacs site search is not working again. Instead of returning errors, it just comes up with Your search did not return any results. The mailing list search is working correctly. -Justin -- Justin A. Lemkul Ph.D.

[gmx-users] g_order for DPC alkyl chain in the micelle

OK Angel, I will contact you off-list SA Dear SA To be honest I am not sure this can be done by using g_angle, I used my own code for this calculation. I could send it to you if you send me a message off the list... but I would prefer to talk with a non-anonymous. Cheers, Ã ngel. --

Re: [gmx-users] g_membed tool

dear mohana, please refer to this page http://wwwuser.gwdg.de/%7Eggroenh/membed.html, to this article http://onlinelibrary.wiley.com/doi/10.1002/jcc.21507/pdf(g_membed: Efficient Insertion of a Membrane Protein into an Equilibrated Lipid Bilayer with Minimal Perturbation) or to this

[gmx-users] g_rmsf

Hi, I am just curious that in the MD community whether there is consensus on how to compare calculated rmsfs and expermental b-factors in x-ray. Should we use average value per residue or one particular atom in a residue for comparsion. Secondly, in NMR, people minimize a number of final

RE: [gmx-users] Memory allocation - xpm2ps

Too bad, I am having this problem with 4.5 now. The xpm file with larger size will counter this problem while smaller ones are fine. Never had any problem with previous version. Chuanyin Shi Department of Chemistry Biochemistry University of Oklahoma

Re: [gmx-users] Memory allocation - xpm2ps

Shi, Chuanyin wrote: Too bad, I am having this problem with 4.5 now. Version 4.5 contains the bug referenced below and was only fixed as of 4.5.2, so make sure you're using the newest version (4.5.3) when reporting problems. In general, fixing problems in old versions is not a high

Re: [gmx-users] lipopeptide problem

Emine Deniz Tekin wrote: Hi GROMACS Users, I am using the GROMACS 4.5.3 version with GROMOS53a6 force field. I simulated a peptide before but this is the first time I am trying to combine a lipid with a peptide (to get a lipo-peptide). I would be really happy if you could help me out with

RE: [gmx-users] Memory allocation - xpm2ps

Ye, I just installed the 4.5.3 and the problem is gone. I was using the 4.5.1 before. Chuanyin Shi Department of Chemistry Biochemistry University of Oklahoma From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A.

[gmx-users] Post simulation energy calculation of Ligand - Protein complex

Hi, I want to calculate the binding energy of ligand-protein complex after simulation. I am running 10ns simulation, please help me out in this regards. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at