Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

It seems that I've fixed that problem by reduce vdv radii for Cl during defining of my box Eventually I've obtained box with the desired density than I've delete vdvradii.dat for my wor dir by when I've launched equilibration I've oibtained Fatal error: Too many LINCS warnings (1598) If you kno

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Mark, I've checked only density value with 500 molecules Ccl4 I have density that is twisely less that I need ( in accordance to the literature ). Also I've checked my box visually and found that the box is not properly tightly packed so I dont know why genbox didnt add some extra mollecules :(

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

On 14/02/2012 4:57 PM, James Starlight wrote: Justin, Firstly I've created the box of desired size with only 500 molecules ( I need 1000) Than I've tried to add extra 200 molecules by means of Genbox genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro but no molecules have been

Re: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Justin, Firstly I've created the box of desired size with only 500 molecules ( I need 1000) Than I've tried to add extra 200 molecules by means of Genbox genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro but no molecules have been added Added 0 molecules (out of 200 requested) of

Re: [gmx-users] Number of windows in umbrella sampling

Thanks Justin. I will try again. But please refer to some protocol if you know and one last question that before doing umbrella sampling simulation how can one be sure that the pulling is good and one should go ahead with selecting window and doing umbrella sampling. In the end when you see histo.x

Re: [gmx-users] zero cut offs

On 14/02/2012 12:55 PM, Juliette N. wrote: On 13 February 2012 20:20, Mark Abraham > wrote: On 14/02/2012 6:26 AM, Juliette N. wrote: Hi all, I have two simple question on in vacu calculations. 1- Say we start from rc=1, and go al

Re: [gmx-users] zero cut offs

On 13 February 2012 20:20, Mark Abraham wrote: > On 14/02/2012 6:26 AM, Juliette N. wrote: > >> Hi all, >> >> I have two simple question on in vacu calculations. >> >> 1- Say we start from rc=1, and go all the way to rc=0.1 then we say cut >> off has been reduced from 1 nm to 0.1 nm meaning that

Re: [gmx-users] zero cut offs

On 14/02/2012 6:26 AM, Juliette N. wrote: Hi all, I have two simple question on in vacu calculations. 1- Say we start from rc=1, and go all the way to rc=0.1 then we say cut off has been reduced from 1 nm to 0.1 nm meaning that atoms fall within 0.1 nm interact with each other. Now when we se

[gmx-users] zero cut offs

Hi all, I have two simple question on in vacu calculations. 1- Say we start from rc=1, and go all the way to rc=0.1 then we say cut off has been reduced from 1 nm to 0.1 nm meaning that atoms fall within 0.1 nm interact with each other. Now when we set rc=0, why dont we consider this as zero cuto

Re: [gmx-users] Noise in a radial distribution function using g_rdf

Fabian Casteblanco wrote: Sorry, I meant on the previous post, using g_rdf On Mon, Feb 13, 2012 at 12:23 PM, Fabian Casteblanco wrote: Hello everyone, I'm using radial distribution functions on gromacs for the first time. Is it normal to see some noise on these plots? You can still see a

Re: [gmx-users] LJ parameter : geometric / arithmetic average

Markus Weingarth wrote: Dear all, Could somebody tell me please, where I can switch from geometric to arithmetic average (for LJ parameter) ? You can't switch within a given force field. Each one is designed for use with a particular method. Page 62 of the 4.5.4 manual. What's taken

[gmx-users] Noise in a radial distribution function using g_rdf

Sorry, I meant on the previous post, using g_rdf On Mon, Feb 13, 2012 at 12:23 PM, Fabian Casteblanco wrote: > Hello everyone, > > I'm using radial distribution functions on gromacs for the first time. >  Is it normal to see some noise on these plots?  You can still see a > trend on the plot but

[gmx-users] Noise in a radial distribution function using g_bar

Hello everyone, I'm using radial distribution functions on gromacs for the first time. Is it normal to see some noise on these plots? You can still see a trend on the plot but it appears somewhat noisy and not as nice and linear as some other plots I've seen in other simulations like the tutoria

[gmx-users] LJ parameter : geometric / arithmetic average

Dear all,Could somebody tell me please, where I can switch from geometric to arithmetic average (for LJ parameter) ?Page 62 of the 4.5.4 manual.What's taken as default ?Thanks a lot.Mark  SMS schreiben mit WEB.DE FreeMail - einfach, schnell und   kostenguenstig. Jetzt gleich testen! http://f.web.de

RE: [gmx-users] g_rdf -surf

By the way, The g(r) = 0.05 is around 1.75 A, which sounds to be consistent with literature, but as r increases towards 10A, instead of converging to a value of 1, g(r) goes towards 41000. I want to return the value of g(r) to 1. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gr

Re: [gmx-users] bug for TIP4P water in GROMACS ?

Mark Abraham wrote: On 14/02/2012 2:23 AM, GZ Zhang wrote: Hi, ALL Has anyone heard that there has been a bug in the energy calculation of TIP4P water in older GROMACS (from v3.3 to v4.0.5) ? Thanks ! Seems wildly unlikely. Actually not: http://www.mail-archive.com/gmx-users@grom

Re: [gmx-users] bug for TIP4P water in GROMACS ?

On 14/02/2012 2:23 AM, GZ Zhang wrote: Hi, ALL Has anyone heard that there has been a bug in the energy calculation of TIP4P water in older GROMACS (from v3.3 to v4.0.5) ? Thanks ! Seems wildly unlikely. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/

[gmx-users] bug for TIP4P water in GROMACS ?

Hi, ALL Has anyone heard that there has been a bug in the energy calculation of TIP4P water in older GROMACS (from v3.3 to v4.0.5) ? Thanks ! Guozhen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at htt

Re: [gmx-users] Umbrella Pulling

Thank you Justin! On Mon, Feb 13, 2012 at 2:44 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Thank you Justin. I run my pulling using two force constant for pulling. >> K1=100 and K1=200 >> Please, see attached plots of force vs time. Is there any criteria to >> adjust pulling con

Re: [gmx-users] Umbrella Pulling

Steven Neumann wrote: Thank you Justin. I run my pulling using two force constant for pulling. K1=100 and K1=200 Please, see attached plots of force vs time. Is there any criteria to adjust pulling constant? Would you suggest running it for a longer time? I know of no systematic study for ch

Re: [gmx-users] Number of windows in umbrella sampling

shahid nayeem wrote: Thanks for quick reply. I have created mutant of a complex by changing interface residue in VMD. These mutant are experimentally known to show less binding affinity. I want to reproduce these results with umbrella sampling. Now I am sending profile and histo file for wt a

Re: [gmx-users] Number of windows in umbrella sampling

shahid nayeem wrote: Dear Justin I am doing umbrella pulling simulation of a protein complex wt and mutant. I expect mutant to give lower deltG value. I am attaching a tif file of energy vs time curve of wt and mutant protein on pulling simulation. These energies are obtained by g_energy and

Re: [gmx-users] how to add potassium

On 14/02/2012 12:38 AM, Weingarth, M.H. wrote: Thank you very much. I managed meanwhile to run the simulation with K+ by adding <<>> to my ffnonbonded.itp I took c6 and c12 parameters (I use gromos 53a6) from Table I of Effect of Force Field Parameters on Sodium and Potassium Ion Bindin

RE: [gmx-users] how to add potassium

Thank you very much. I managed meanwhile to run the simulation with K+ by adding <<>> to my ffnonbonded.itp I took c6 and c12 parameters (I use gromos 53a6) from Table I of Effect of Force Field Parameters on Sodium and Potassium Ion Binding to Dipalmitoyl Phosphatidylcholine Bilayers ' As

Re: [gmx-users] Umbrella Pulling

Steven Neumann wrote: Dear Gmx Users, Is it always required to restrained positions of the protein while pulling your ligand? My system is made of 10 ligands attached to my protein surface. I am pulling one of them. No, it is not required. I assume you've gotten this idea from my tutoria

Re: [gmx-users] lipid tutorial problem

prashant kurkute wrote: Dear all, I am very new to GROMACS. The my problem may be a very basic and stupid but very big for me!!.. I am performing Justin Lemkul Lipid tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html) and I am upto

Re: [gmx-users] lipid tutorial problem

On 13/02/2012 8:54 PM, prashant kurkute wrote: Dear all, I am very new to GROMACS. The my problem may be a very basic and stupid but very big for me!!.. I am performing Justin Lemkul Lipid tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index

Re: [gmx-users] how to add potassium

On 13/02/2012 9:32 PM, Weingarth, M.H. wrote: Dear all, I do not manage to add potassium ions to my system correctly. I foraged in the mailing list and tried to follow all advices, but it does not work out for me. It would be great if anybody could give me some advice. (here my so-far futil

Re: [gmx-users] Forcefield question

On 13/02/2012 9:46 PM, Matthias Ernst wrote: Hi, I am currently working with the AMBER forcefields provided by GROMACS. I noticed there are atoms in the forcefields (e.g. amber99 or amber03) with LJ parameters of 0.0 for sigma and epsilon. For example, the HO atom type is sometimes used (e.g.

Re: [gmx-users] installation problem of gromacs 4.0.7 on Rocks cluster

On 13/02/2012 9:56 PM, Parul tew wrote: Dear Gmx Users, I am facing problem while installing gromacs 4.0.7 on the rocks cluster 1. command: ./configure --enable-float --enable-threads --enable-sse --enable-mpi If you were using an up-to-date version of GROMACS (and it is likely that you shou

Re: [gmx-users] problem with index file

On 13/02/2012 11:00 PM, Anushree Tripathi wrote: How could we add DPPC group (for 6400 atoms) in index file?I have gone through the gromacs tutorial (http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx) but not getting exactly. make_ndx -f your_coordinate_file_containing_DPPC.gro -n

[gmx-users] problem with index file

How could we add DPPC group (for 6400 atoms) in index file?I have gone through the gromacs tutorial (http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx) but not getting exactly. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Plea

[gmx-users] problem with NVT equilibration

Shall we use 'residuetypes.dat' file in 'grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o em.tpr' command without creating index file? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.

[gmx-users] Forcefield question

Hi, I am currently working with the AMBER forcefields provided by GROMACS. I noticed there are atoms in the forcefields (e.g. amber99 or amber03) with LJ parameters of 0.0 for sigma and epsilon. For example, the HO atom type is sometimes used (e.g. in SER or in the terminal Hs of DNA residues

[gmx-users] installation problem of gromacs 4.0.7 on Rocks cluster

Dear Gmx Users, I am facing problem while installing gromacs 4.0.7 on the rocks cluster 1. command: ./configure --enable-float --enable-threads --enable-sse --enable-mpi we got the following error: checking for cc... cc checking for C compiler default output file name... a.out checking whether t

[gmx-users] how to add potassium

Dear all, I do not manage to add potassium ions to my system correctly. I foraged in the mailing list and tried to follow all advices, but it does not work out for me. It would be great if anybody could give me some advice. (here my so-far futile- procedure) 1

[gmx-users] lipid tutorial problem

Dear all, I am very new to GROMACS. The my problem may be a very basic and stupid but very big for me!!.. I am performing Justin Lemkul Lipid tutorial (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html) and I am upto the 3rd stage. But after gi

[gmx-users] Umbrella Pulling

Dear Gmx Users, Is it always required to restrained positions of the protein while pulling your ligand? My system is made of 10 ligands attached to my protein surface. I am pulling one of them. I have just seen trajectory of pulling my ligand without restraining positions of protein and 9 remainin