RE: [gmx-users] free energy decomposition

Hi, Currently you can only get a decomposition every nstlog steps in the log file with the mdrun option -seppot. However, only the sum of VdW and Coulomb will be reported. Berk Date: Tue, 3 Feb 2009 16:16:55 +0800 From: friendli2...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users]

RE: [gmx-users] how to calculate the viscosity of the bulk

Hi, This Einstein method of g_energy is extremely sensitive to the system setup. You should have perfect pressure fluctuations, which probably means shifted LJ potential, PME, constant volume and double precision. Some time ago I made a comparison of different methods:

[gmx-users] segmentation fault

Respectable Mark/David/Berk   I want to study diffusion of oxygen in water at constant pressure of 1 bar. I thus coupled my system with berendsen with the reference pressureof 1 bar. But my production run gave a segmentation fault.   But when I don't couple, it doesn't. What should I do?   Your

Re: [gmx-users] segmentation fault

Sunil Thapa wrote: Respectable Mark/David/Berk I want to study diffusion of oxygen in water at constant pressure of 1 bar. I thus coupled my system with *berendsen* with the reference pressureof 1 bar. But my production run gave a segmentation fault. But when I don't couple, it doesn't.

[gmx-users] constructing polymer.itp files from monomer files obtained from prodrg server

Dear all, Am trying for a simulation with polymers on a lipid bilayer.when i give the entire polymer file which consists of 228 atoms to prodrg server for generating itp files its taking only a block of polymer as input and generating itp files for that polymer alone.I have two different monomer

RE: [gmx-users] free energy with TIP4P bug fixed

Hi, There are three ways to avoid this bug with free-energy and TIP4P: Or make sure that any energy group that contains perturbed atoms does not include any non-perturbed atoms with charges, or use GMX_NO_SOLV_OPT (slow), or use the fix below. Berk RCS file: /home/gmx/cvs/gmx/src/mdlib/ns.c,v

[gmx-users] set up self assembly for mixture of lipids using genbox

Hello I am trying to using genbox to set up a random 2-lipid mixture. Is there a way to do this? First, i put 100 POPC molecules randomly in the sim. box. Now I want to add 28 POPS lipids. How can I do this ? thank you for helping out -Maria -- Maria G. Technical University of Denmark

Re: [gmx-users] set up self assembly for mixture of lipids using genbox

maria goranovic wrote: Hello I am trying to using genbox to set up a random 2-lipid mixture. Is there a way to do this? First, i put 100 POPC molecules randomly in the sim. box. Now I want to add 28 POPS lipids. How can I do this ? I'm not aware of a direct method for doing this. Creating

Re: [gmx-users] Martini + other force field

On Mon, Feb 2, 2009 at 7:50 PM, XAvier Periole x.peri...@rug.nl wrote: -No: is where you can find much more arguments. First of all the two force fields have not been parametrized consistently. Second you'll probalby have problems in defining the interactions between the two approches. How

RE: [gmx-users] free energy with TIP4P bug fixed

dear Berk, please let us know whether following patch is correct for 3.3.1 diff orig-ns.c ns.c 2c2 * $Id: ns.c,v 1.84.2.3 2006/03/01 07:57:46 spoel Exp $ --- * $Id: ns.c,v 1.84.2.3.1 2009/02/03 20:27:00 hess Exp $ 617c617 bool bDoVdW_i,bDoCoul_i; --- bool

Re: [gmx-users] Martini + other force field

On Feb 3, 2009, at 4:03 PM, Elton Carvalho wrote: On Mon, Feb 2, 2009 at 7:50 PM, XAvier Periole x.peri...@rug.nl wrote: -No: is where you can find much more arguments. First of all the two force fields have not been parametrized consistently. Second you'll probalby have problems in

Re: [gmx-users] Martini + other force field

Am I wrong, or are you considering some kind of MSCG (which is not into gromacs at least in a standard, straight forward out of the box way)? That's nice, would be really interesting to implement, would take long time and is still a relativelly open-field with lot to be still explored. I think we

[gmx-users] Re: set up self assembly for mixture of lipids using genbox

That sounds like a good idea. However, what sort of cheap physical model are you suggesting to get rid of the very ordered initial state ? -Maria maria goranovic wrote: Hello I am trying to using genbox to set up a random 2-lipid mixture. Is there a way to do this? First, i put 100

[gmx-users] buckingham pairs

I'm trying to use the Buckingham potential in my simulation. First, I've selected [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 2 2 no 0.00.0 and then in atomtype I've put A,B,C as needed by that potential. But I have some

[gmx-users] RPM and double precision

Hello, We have installed GROMACS 3.3.3 using rpm. Apparently the default installation is single precision. We would like to use double precision. How do you run rpm again such that it installs the double precision version of GROMACS? Not sure what the rpm syntax would be to do this.

RE: [gmx-users] RPM and double precision

Hi, The rpm's are only in single precision, because for nearly all purposes that suffices (some precision critical parts of the code are always in double precision). Are you sure your require double precision? If so, you will need to compile Gromacs yourself. Berk From:

[gmx-users] langevin dynamics and manual

Hello, I have a comment regarding the Gromacs manual. For equation (3.62) in Chapter 3.8, \epsilon_i is called the friction constant. This is incorrect since in that equation \epsilon is actually collision frequency and should be represented with the letter \gamma. The product of the collision

[gmx-users] RPM and double precision

Berk, I'm not sure if we really need double precision. Frankly, I would rather not fool with it. However, when we run pdb2gmx -f compound4.pdb -p compound4.top -o compound4_a.pdb grompp -f compound4.mdp -c compound4_a.pdb -p compound4.top -o compound4.tpr -zero mdrun -v -s compound4.tpr -o

[gmx-users] is the tip4p MW velocity treated differently in gromacs 3 vs 4

Hello, Does anybody know if there is a reason why the .gro output velocities would be different for tip4p MW in a zero-step mdrun between gromacs 3 and gromacs 4 (3.3.1 and 3.3.3 are the same, and are different from 4.0.2 and 4.0.3, which are themselves the same). diff gmx4.0.3/feoff.gro

[gmx-users] is the tip4p MW velocity treated differently in gromacs 3 vs 4

Thanks David, you are correct about initial step constraints. More information inline below, but my question has been resolved. Chris Neale wrote: Hello, Does anybody know if there is a reason why the .gro output velocities would be different for tip4p MW in a zero-step mdrun between

Re: [gmx-users] is the tip4p MW velocity treated differently in gromacs 3 vs 4

Chris Neale wrote: Hello, Does anybody know if there is a reason why the .gro output velocities would be different for tip4p MW in a zero-step mdrun between gromacs 3 and gromacs 4 (3.3.1 and 3.3.3 are the same, and are different from 4.0.2 and 4.0.3, which are themselves the same). Is this

[gmx-users] Free energy perturbation of Cu(I) binding

Hi all, Thank you for the help till now and I successfully generated the forcefield Cu(I) binding protein. Now I wanted get the structure of non-copper bound form which I think I can do by perturbing the charge on Cu(I) and even perturbing the bonded and nonbonded parameters. Is there a

[gmx-users] is the tip4p MW velocity treated differently in gromacs 3 vs 4

contrary to my previous stament, I am no longer convinced that it is simply an initial constraints issue. In my last post, I stated: when I define -DFLEXIBLE and make the tpr using gromacs 3 and then run using gromacs 4, I do get gromacs 4 - identical velocities.. However, thinking more on

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Perhaps this is obvious, but typically you only want to do free energy perturbation if you are interested in computing a free energy difference. If you are merely interested in structural properties of a different system (in this case, the protein without the copper there) you can simply make the

[gmx-users] Missing atom error when using some force fields

Dear all, I am new to MD simulation. I am trying to do an all-atom MD simulation with explicit water of a protein which has a few missing side-chain atoms of a GLN residue. 1. Which force field would you recommend? The protein is an x-ray crystal structure, about 200 residues. Hydrogen atoms and

Re: [gmx-users] Missing atom error when using some force fields

Peggy Yao wrote: Dear all, I am new to MD simulation. I am trying to do an all-atom MD simulation with explicit water of a protein which has a few missing side-chain atoms of a GLN residue. 1. Which force field would you recommend? The protein is an x-ray crystal structure, about 200

Re: [gmx-users] Re: set up self assembly for mixture of lipids using genbox

maria goranovic wrote: That sounds like a good idea. However, what sort of cheap physical model are you suggesting to get rid of the very ordered initial state ? Cut-off electrostatics with a short cut-off will be cheap and dodgy enough for the purpose. One could play with NPT at low

[gmx-users] Re: Benchmarks for 4.0.X

That would be right, just find it after you sent the message. Have found one now: http://www.hpcx.ac.uk/research/biochemistry/gromacs.html Catch ya, Dallas Warren Monash University winmail.dat___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] Benchmarks for 4.0.X

Have these been done yet? Been trying to find some, found a few individual tests, but nothing like http://www.gromacs.org/content/view/24/37/ Catch ya, Dallas Warren Monash University winmail.dat___ gmx-users mailing listgmx-users@gromacs.org

[gmx-users] RE: Benchmarks for 4.0.X

And for future reference of others, also some good data in the GROMACS 4 paper, funny enough ;-) GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput., 2008, 4 (3), pp 435–447 DOI: http://dx.doi.org/10.1021/ct700301q Catch ya,

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Thanks David, But if I just remove the Copper atom and do the simulation as copper is charged there would be sudden change in electrostatics and the protein started unfolding when I ran the simulation for 10ns. So I thought perturbing the charge by little every time I can get a structure with more

Re: [gmx-users] Free energy perturbation of Cu(I) binding

abhigna polavarapu wrote: Thanks David, But if I just remove the Copper atom and do the simulation as copper is charged there would be sudden change in electrostatics and the protein started unfolding when I ran the simulation for 10ns. So I thought perturbing the charge by little every time I

Re: [gmx-users] Free energy perturbation of Cu(I) binding

Thanks Mark, thats what I really wanted to do. So can you please let me know where I can find out the way to do position restraints and to know how these work. abhigna On Tue, Feb 3, 2009 at 10:18 PM, Mark Abraham mark.abra...@anu.edu.au wrote: abhigna polavarapu wrote: Thanks David, But if I

Re: [gmx-users] Free energy perturbation of Cu(I) binding

abhigna polavarapu wrote: Thanks Mark, thats what I really wanted to do. So can you please let me know where I can find out the way to do position restraints and to know how these work. Chapter 5 in the manual, or some tutorial material (perhaps from the wiki). Mark

[gmx-users] monoclinic super cell

Hi, I am simulating monoclinic hydroxyapatite CA10 (PO4)6 (OH)2. I have found a PDB of CA5 (PO4)3 (OH) , whitch consits of 22 atoms. the monoclinic structure of HAP has however 88 atoms and space group (P 21/b) it means to generate the super cell of HAP i have to feed editconf with the

[gmx-users] monoclinic super cell

Hi, I am simulating monoclinic hydroxyapatite CA10 (PO4)6 (OH)2. I have found a PDB of CA5 (PO4)3 (OH) , whitch consits of 22 atoms. the monoclinic structure of HAP has however 88 atoms and space group (P 21/b) it means to generate the super cell of HAP i have to feed editconf with the

[gmx-users] monoclinic super cell

Hi, I am simulating monoclinic hydroxyapatite CA10 (PO4)6 (OH)2. I have found a PDB of CA5 (PO4)3 (OH) , whitch consits of 22 atoms. the monoclinic structure of HAP has however 88 atoms and space group (P 21/b) it means to generate the super cell of HAP i have to feed editconf with the

[gmx-users] monoclinic super cell

Hi, I am simulating monoclinic hydroxyapatite CA10 (PO4)6 (OH)2. I have found a PDB of CA5 (PO4)3 (OH) , whitch consits of 22 atoms. the monoclinic structure of HAP has however 88 atoms and space group (P 21/b) it means to generate the super cell of HAP i have to feed editconf with the

[gmx-users] monoclinic super cell

Hi, I am simulating monoclinic hydroxyapatite CA10 (PO4)6 (OH)2. I have found a PDB of CA5 (PO4)3 (OH) , whitch consits of 22 atoms. the monoclinic structure of HAP has however 88 atoms and space group (P 21/b) it means to generate the super cell of HAP i have to feed editconf with the

[gmx-users] monoclinic super cell

Hi, I am simulating monoclinic hydroxyapatite CA10 (PO4)6 (OH)2. I have found a PDB of CA5 (PO4)3 (OH) in internet , whitch consits of 22 atoms. the monoclinic structure of HAP has however 88 atoms and space group (P 21/b) it means to generate the super cell of HAP i have to feed editconf with the

[gmx-users] g_hbond problem to select donor atoms in drug

Dear Gromacs users, I am trying to analyze hydrogen bonding between a Protein and Drug by g_hbond from .xtc and .tpr and .ndx files. I am getting expected results when the H-bond donor and the hydrogen atom is from protein while the hydrogen bond acceptor atom is in the drug. The results are,

Re: [gmx-users] g_hbond problem to select donor atoms in drug

geeta kant wrote: Dear Gromacs users, I am trying to analyze hydrogen bonding between a Protein and Drug by g_hbond from .xtc and .tpr and .ndx files. I am getting expected results when the H-bond donor and the hydrogen atom is from protein while the hydrogen bond acceptor atom is in the

[gmx-users] Fatal error: Could only find a forcefield type for 106 out of 270 atoms

Could you please let me know why GROMACS is able to find forcefields for only 106 of the 270 atoms. My .gro file is a model of a graphene structure with 211 equally spaced carbon atoms with the remaining hydrogen atoms also equally spaced from the carbon atoms to which they are bonded. Here is a

[gmx-users] analyzing beta factor

Hi users, I want to plot beta factor versus residue number plot at the analyzing part.I read manual and search in the web but I could not find a reasonable result for this plot.I wonder if anybody know about it. Thank you, Özge ___

Re: [gmx-users] g_hbond problem to select donor atoms in drug

Mark Abraham wrote: geeta kant wrote: Dear Gromacs users, I am trying to analyze hydrogen bonding between a Protein and Drug by g_hbond from .xtc and .tpr and .ndx files. I am getting expected results when the H-bond donor and the hydrogen atom is from protein while the hydrogen bond

Re: [gmx-users] analyzing beta factor

özge kül wrote: Hi users, I want to plot beta factor versus residue number plot at the analyzing part.I read manual and search in the web but I could not find a reasonable result for this plot.I wonder if anybody know about it. What is the beta factor? Thank you, Özge

Re: [gmx-users] Fatal error: Could only find a forcefield type for 106 out of 270 atoms

darre...@ece.ubc.ca wrote: Could you please let me know why GROMACS is able to find forcefields for only 106 of the 270 atoms. My .gro file is a model of a graphene structure with 211 equally spaced carbon atoms with the remaining hydrogen atoms also equally spaced from the carbon atoms to which

Re: [gmx-users] is the tip4p MW velocity treated differently in gromacs 3 vs 4

Chris Neale wrote: contrary to my previous stament, I am no longer convinced that it is simply an initial constraints issue. There are two things to do: 1. run gmx3.3 and gmx4.0 with the 3.3 tpr file. This should give the same result in principle. 2. run gmx3.3 and gmx4.0 with their own tpr