Re: [gmx-users] umbrella sampling pull_group0 adn pull_group1

You should define the proper groups in your index file. Then put their names into pull_group0 and pull_group1 of the mdp file. On Thu, Jun 30, 2011 at 9:21 AM, sreelakshmi ramesh < sree.laks...@research.iiit.ac.in> wrote: > Dear all, > i wanted to do umbrella sampling on petide which is

[gmx-users] umbrella sampling pull_group0 adn pull_group1

Dear all, i wanted to do umbrella sampling on petide which is completely folded.now in mdp file there is a option pull_group0 and pull_group1 i just know the ref group and the one to which pulling force has to be applied in pdb file their atom numbers are 201 adn 61 .how should i ment

[gmx-users] micelle clustering

Hi all, I have simulated a system of randomly dispersed surfactants in water using gromacs (4.0.7) for about 100 ns MD. Micelles are formed after around 40 ns. I am using a time step of 0.002 fs with xtc files written every 500 steps. For analyzing the micellar properties, I tried the commands gi

Re: [gmx-users] CPHMD in GROMACS4.5

On 30/06/2011 3:55 PM, Anirban Ghosh wrote: Hi ALL, Is it possible to run constant pH MD simulation (CPHMD) in Gromacs4.5? Any suggestion is welcome. Thanks, Anirban See http://www.gromacs.org/Documentation/FAQs Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.o

[gmx-users] CPHMD in GROMACS4.5

Hi ALL, Is it possible to run constant pH MD simulation (CPHMD) in Gromacs4.5? Any suggestion is welcome. Thanks, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_

Re: [gmx-users] error in running pdb2gmx command

On 30/06/2011 1:48 PM, rashi parihar wrote: thanx @justin..I have seen gromacs web site before posting..the solution of my problem was written in gromacs website was " the atom names are expected to match those found in the .rtp file that define the

Re: [gmx-users] error in running pdb2gmx command

thanx @justin..I have seen gromacs web site before posting..the solution of my problem was written in gromacs website was " the atom names are expected to match those found in the .rtp file that define the building block(s) in your struct

Re: [gmx-users] Question about g_bar output

Warren Gallin wrote: Justin, OK, this makes sense to me, and I can do the interconversion of units easily enough outside of the GROMACS tools. Should I file a bug report? No need. I've fixed this in the release-4-5-patches branch so the output will be correct whenever ve

Re: [gmx-users] Question about g_bar output

Justin, OK, this makes sense to me, and I can do the interconversion of units easily enough outside of the GROMACS tools. Should I file a bug report? Warren Gallin On 2011-06-29, at 12:48 PM, Justin A. Lemkul wrote: > > > Warren Gallin wrote: >> Hi, >> I've just run g_b

Re: [gmx-users] Question about g_bar output

Warren Gallin wrote: Hi, I've just run g_bar on data from a simulation, and I am having trouble reconciling the graphical output with the numerical output. The units seem to be inconsistent. In particular the numbers under detailed results are in units of kT, followed by f

[gmx-users] Question about g_bar output

Hi, I've just run g_bar on data from a simulation, and I am having trouble reconciling the graphical output with the numerical output. The units seem to be inconsistent. In particular the numbers under detailed results are in units of kT, followed by final results in kJ/mole (

Re: [gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

One of my issues is now solved. As you guessed, the PBD was in an improper format. After solving this small issues, I read about the need for an lipids.itp and pope.itp file. I found these tutorial (link below) for the itp file construction. Can I adept these steps for the construction of corre

Re: [gmx-users] Re:Re: Tabulated potential for metal-oxide (Mark Abraham)

On 29/06/2011 7:08 PM, manana koberidze wrote: Thank you Mark, what puzzles me here is summation, if it was only one term than it would be clear. But a normal Coulomb interaction has the form E_i = q_i * SUM{q_j / r_ij} summing over the other atoms j. If you can cast the electrostatic compone

[gmx-users] protonated histidine with Martini

Dear gromacs users, I want to use Martini force field for my simulation. The simulation is supposed to be performed at acidic environment (pH2.6). In this environment His is protonated. I want to add protonate Hisidine in itp file. Where exactly should I put the charge on S2c or on S3c? Mayb

Re: [gmx-users] minimization problem (Martini simulation)

Thank you very much. It worked. Regina Quoting "Justin A. Lemkul" : pol...@fh.huji.ac.il wrote: Dear Justin, Thank you very much for your answer. Can you please explain me what do you mean by saying "EM wasn't sufficient". What information do you need in order be able to help? I run EM wit

Re: [gmx-users] error in running pdb2gmx command

rashi parihar wrote: HI all ..while running pdb2gmx command .I am getting error "Fatal error: Atom CT in residue TYR 314 was not found in rtp entry TYR with 20 atoms while sorting atoms" .what this error mean and how can I rectify this problem?plz help me. Please search the mailing list arc

[gmx-users] error in running pdb2gmx command

HI all ..while running pdb2gmx command .I am getting error "Fatal error: Atom CT in residue TYR 314 was not found in rtp entry TYR with 20 atoms while sorting atoms" .what this error mean and how can I rectify this problem?plz help me. -- [image: images[12]] “Many Smiles Begin Because Of Anothe

Re: [gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

Leonhard Henkes wrote: Thanks for your reply, my whole pdb file includes an equilibrated membrane bilayer, constructed with VMD for NAMD. I used the CHARMM27 FF while constructing it. Now, I wanted to convert this system for a run in Gromacs. To solve my issus, I divided my system into four

Re: [gmx-users] Re: Running Lyz in water

Ravi Kumar Venkatraman wrote: Dear all, I am not finding mistake in that tutorial but I wanted to know where did I go wrong. Until generation of topology for protein there was no problem (I cross checked with the tutorial). After that I edited the box of protein as such.

[gmx-users] Re: Running Lyz in water

Dear all, I am not finding mistake in that tutorial but I wanted to know where did I go wrong. Until generation of topology for protein there was no problem (I cross checked with the tutorial). After that I edited the box of protein as such. After generating the solvation box I h

Re: [gmx-users] Iusses while converting a POPE pdb with pdb2gmx and ff charmm27

Thanks for your reply, my whole pdb file includes an equilibrated membrane bilayer, constructed with VMD for NAMD. I used the CHARMM27 FF while constructing it. Now, I wanted to convert this system for a run in Gromacs. To solve my issus, I divided my system into four new pdb's (ion, water, lipi

[gmx-users] Re:Re: Tabulated potential for metal-oxide (Mark Abraham)

Thank you Mark, what puzzles me here is summation, if it was only one term than it would be clear. Generally, if there is no other way than changing the source code which files must be modified?Is there any information about it anywhere? I found just the list of files but for bonded interaction in

Re: [gmx-users] Running Lyz in water

On 06/29/2011 04:18 PM, Ravi Kumar Venkatraman wrote: Dear all, I have been running lyz in water. I have 20 ps pre-equilibrated NVT and 200 ps NPT configuration of spce216 water. I am following the instruction from gromacs tutorial. This is the link for the tutorial, http://www.b

[gmx-users] implicit solvent and generic interaction

Dear GROMACS experts: I'm using a GB implicit solvent function in ver. 4.5.4. When I switched on GMX_NB_GENERIC with implicit_solvent=GBSA, I've got the message, "Fatal error: Death & horror! GB generic interaction not implemented". I'm wondering that is it difficult to add some code to nb_generi