[gmx-users] simulation of DNA model

Dear all I want to ask one basic question i.e is it possible to do simulation of DNA model with gromacs ? If it possible which force field will be suitable for this? I am waiting for yours reply. thanks a lot in advance. Nitu sharma __

[gmx-users] local pressure calculation

Dear Sir, I want to calculate local pressure of the bilayer membrane. I see from the mailing list and earlier paper that it was done by gromacs-locap-3.0.2. Could you please tell me that this package will assist with gromacs 3.3.3 or gromacs 4.0.4 version. Is there any other option to c

RE: [gmx-users] local pressure

I would recommend you have a read through the appendix in the GROMACS manual titled "Manual Pages". This has all the scripts provided with GROMACS and the manual page for them, which describes what each one does. Reading through that will go a long way to letting you know what you can and can't d

[gmx-users] local pressure

Dear Sir, I would like to calculate local pressure of the bilayer membrane. Is it possible to do by new version of gromacs. could you please assist me to do it. After simulating bilayer m,embrane, I found trr, edr files. Thanking you , Anirban ___

RE: [gmx-users] lateral stress and surface tension

http://www.gromacs.org/pipermail/gmx-users/2006-December/024953.html Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology and Pharmacology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167

[gmx-users] lateral stress and surface tension

Dear Sir, I am analysing bilayer membrane. Could you please tell me how I can calculate stress and surface tension of the membrane? Thanking you, Anirban ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listi

Re: [gmx-users] want to calculate pressure from virial

anirban polley wrote: Dear Sir, I want to calculate virial, hence pressure. PV=NKT-1/3 * < sum of (r * f)> where r is displacement and f is internal force. Now, how can I proceed? 1. g_traj -f name.trr -af gives me force and each velocity with time? Now, question, is the f

[gmx-users] want to calculate pressure from virial

Dear Sir, I want to calculate virial, hence pressure. PV=NKT-1/3 * < sum of (r * f)> where r is displacement and f is internal force. Now, how can I proceed? 1. g_traj -f name.trr -af gives me force and each velocity with time? Now, question, is the force given in data is only

Re: [gmx-users] virtual sites

zhang wrote: Dear users, I use the Cationic Dummy Atom methods by Pang to simulate a protein containing Zn2+. How to get the parameters in [ virtual_sites? ] section? I use the model 4fd. In the following example, how to get the value of parameters a, b and d? [ virtual sit

[gmx-users] virtual sites

Dear users, I use the Cationic Dummy Atom methods by Pang to simulate a protein containing Zn2+. How to get the parameters in [ virtual_sites? ] section? I use the model 4fd. In the following example, how to get the value of parameters a, b and d? [ virtual sites4 ] ;

Re: [gmx-users] DNA-ligand interactions with AMBER

Paulo Netz wrote: Dear Gromacs users I am simulating the interactions between ligands and DNA using GROMACS with the AMBER force field, as implemented with the AMBER PORT for GROMACS. Simulating DNA is actually very easy with this protocol, but for the ligand some problems arise. Until now we ar

[gmx-users] DNA-ligand interactions with AMBER

Dear Gromacs users I am simulating the interactions between ligands and DNA using GROMACS with the AMBER force field, as implemented with the AMBER PORT for GROMACS. Simulating DNA is actually very easy with this protocol, but for the ligand some problems arise. Until now we are constructing the t

Re: [gmx-users] protein falls apart in energy minimization

Zhong Zheng wrote: Thanks. That solves the problem. But I still see this warning message: Steepest Descents did not converge to Fmax < 10 in 201 steps. Potential Energy = -1.2866480e+05 Maximum force = 3.4851584e+03 on atom 3683 Norm of force = 6.3128883e+01 That means I should ru

Re: [gmx-users] protein falls apart in energy minimization

Thanks. That solves the problem. But I still see this warning message: Steepest Descents did not converge to Fmax < 10 in 201 steps. Potential Energy = -1.2866480e+05 Maximum force = 3.4851584e+03 on atom 3683 Norm of force = 6.3128883e+01 That means I should run longer energy minimiz

[gmx-users] DNA-ligand simulation with AMBER FF

Dear Gromacs Users I am simulating the interactions between ligands and DNA using GROMACS with the AMBER force field, as implemented with the AMBER PORT for GROMACS. Simulating DNA is actually very easy with this protocol, but for the ligand some problems arise. Until now we are constructing the

[gmx-users] No default LJ-14 types

Dear GROMACS users, I want to use GROMOS force field for the polyethylene simulations to compare the performance of this force field with those generated for alkanes. I have prepared my own files based on the ffG53a5 files. In itp I used [ defaults ] ; nbfunccomb-rule gen-pairs

[gmx-users] CG to Atomistic

Hello all! I found the answer on: http://md.chem.rug.nl/~marrink/MARTINI/Tutorial.html Best regards, Edson. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.

RE: [gmx-users] UA simulation of PEO melt

Hi Patrick, Thank you very much for your response. I have just downloaded the paper of which you sent the reference. I have not found other FF parameters except for the torsional one about the C-C bond. I have also some papers which provide good results on PEO simulations (JCP, 124, 234901 (2006);

Re: [gmx-users] UA simulation of PEO melt

Hi Zuzana, I'm actually working on the paramaterization of polyethers with the GROMOS developers. Currently in G53a?, there's no such torsion O-C-C-O in GROMOS and I don't advice to use any combination of existing monoethers. I could figure out that they give the wrong free energy of hydration

[gmx-users] Re: Require help in GROMACS

It would be best to post this message on the gmx-users list. It is a Gromacs-related error message, and not specific to my tutorial. It is an oft-encountered error, resulting from incorrect updating of your topology. InflateGRO *did* remove lipids; check the screen output carefully. Here's

Re: [gmx-users] TIP5P - dummies sit on top of each other

ilona.bal...@bioquant.uni-heidelberg.de wrote: Hi, I am trying to change my ice crystal from a three-site water model to the TIP5P water model. For that I use pdb2gmx. The program adds the two dummy atoms, but they are at exactly the same position as the oxygen and not two additional sites a

[gmx-users] g_cluster matrix input

Hello, I think that it would be useful to clusterize any kind of values with g_cluster. However the only way I found to input values from an external matrix is in xpm format. Is there a way to input to g_cluster a square matrix of numbers, so that it keeps the actual values and it doesn't approx

[gmx-users] CG to Atomistic

Hello all! I would like to know if anybody already know a way to convert a protein.pdb in course-grain to atomistic model? This protein was previus atomistic, but now I am working with its course-grain state to improve my analysis. best regards, Edson. ___

Re: [gmx-users] TIP5P - dummies sit on top of each other

ilona.bal...@bioquant.uni-heidelberg.de wrote: Hi, I am trying to change my ice crystal from a three-site water model to the TIP5P water model. For that I use pdb2gmx. The program adds the two dummy atoms, but they are at exactly the same position as the oxygen and not two additional sites

RE: [gmx-users] Re: v-rescale - harmonic oscillator

Hi, I have an optimal leap-frog v-rescale thermostat implemented for CVS head. This will be in Gromacs 4.1. Gromacs 4.1 will probably also have a velocity verlet integrator, for which we can also remove the last very small drift in the v-rescale implementation. Berk > From: servaas.michielss..

[gmx-users] TIP5P - dummies sit on top of each other

Hi, I am trying to change my ice crystal from a three-site water model to the TIP5P water model. For that I use pdb2gmx. The program adds the two dummy atoms, but they are at exactly the same position as the oxygen and not two additional sites as stated by the paper and also as I find in

[gmx-users] Re: v-rescale - harmonic oscillator

Dear Dr. Bussi, Thank you very much for the explanation of this problem. So I understand that a problem remains with the integrator used in GROMACS for small systems and that Berk is fixing this (and also a small error is comming from using leap frog instead of velocity verlet). I don't use th

Re: [gmx-users] No default Angle types

darre...@ece.ubc.ca wrote: Hi Justin, Thanks for the quick reply. Yes, I was also thinking about using a different atom type such as the alkane types you mentioned below. However, when I thought about how I can include these atom types in my .n2t file, I recognized that this might cause a pote

[gmx-users] UA simulation of PEO melt

Dear GROMACS users I want to run simulations of polyethyleneoxide melt. In literature I have found united atoms force fields that performed well for this kind of simulation. For dihedral potential I need to extend the Ryckaert-Bellemans potential up to the order of six. I have looked at the mailin

Re: [gmx-users] lipid_posre.itp file

Hi Nitu You cab use the Gromacs tool genrest. Nuno On Tue, 2009-05-12 at 12:28 +0530, nitu sharma wrote: > Dear all > > I need lipid_posre.itp file can anyone suggest me > from where I can find it ?or If I have to make it by my own then > please let me know how can I make it

Re: [gmx-users] Re: Problem with protein in lipid bilayer simulation

Hello Anirban, This is due to some wrong editing and modifications of the .itp files. Please follow the tutorial carefully. The explanation for each modification is also given quite clearly. Regards, Pawan On Tue, May 12, 2009 at 2:26 PM, Anirban Ghosh wrote: > Hello Pawan and Justin, > > Thank

[gmx-users] Re: Problem with protein in lipid bilayer simulation

Hello Pawan and Justin, Thanks for the reply. I have removed the HW entries from the ffG53a6nb_lipid.itp file and still getting the error: -- Fatal error: Unknown atomtype OW --

Re: [gmx-users] problem with the creating of a top-file

Saskia Frenzel wrote: Dear all, I have a problem with the creating of a top-file because the following error appeared: Fatal error: [ file spc.itp, line 32 ] Atom index (1) in bonds out of bounds (1-0). This probably means that you have inserted topologie section "settles" in a part belonging

[gmx-users] problem with the creating of a top-file

Dear all, I have a problem with the creating of a top-file because the following error appeared: Fatal error: [ file spc.itp, line 32 ] Atom index (1) in bonds out of bounds (1-0). This probably means that you have inserted topologie section "settles" in a part belonging to a different molecule

[gmx-users] Re: v-rescale - harmonic oscillator

Dear Servaas, the problem that you found is not related to the stochastic rescaling itself, but to the way the effective energy is calculated in gromacs. In particular, the increment in the integral part is not consistent with the applied scaling. You can correct for this by changing src/mdlib/cou

Re: [gmx-users] lipid_posre.itp file

nitu sharma wrote: Dear all I need lipid_posre.itp file can anyone suggest me from where I can find it ?or If I have to make it by my own then please let me know how can I make it. If anyone can suggest me I really will be thankful for him. Start here http://wiki.gromacs