Re: [gmx-users] NVT conserved-energy lysozyme

On 15/05/2012 6:17 PM, David de Sancho wrote: Dear all I have been following Justin Lemkul's tutorial for the lysozyme simulations http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html I am using Gromacs 4.5.5. My concern is with the energy conservation in the

Re: [gmx-users] Two [ dihedrals ] sections in topology

On Tue, 2012-05-15 at 15:43 +0100, Lara Bunte wrote: Hi You wrote: Two blocks of dihedrals are normal output for pdb2gmx - one for proper and one for improper dihedrals. Is there a way to force pdb2gmx that there is only my block with improper dihedrals in the topology? Not that

Re: [gmx-users] Two [ dihedrals ] sections in topology

On 5/15/12 10:43 AM, Lara Bunte wrote: Hi You wrote: Two blocks of dihedrals are normal output for pdb2gmx - one for proper and one for improper dihedrals. Is there a way to force pdb2gmx that there is only my block with improper dihedrals in the topology? Normally pdb2gmx will

Re: [gmx-users] topology file in DPPC

On 5/15/12 10:47 AM, scapr...@uniroma3.it wrote: Dear all, I'm meticulously following the tutorial KALP-15 in DPPC in order to carry on the simulation of a protein of mine in a extended patch of DPPC. I have already modified the ffnonbonded.itp and ffbonded.itp. At this point I'm reading that

[gmx-users] parameters and restrains for Fe3+

Hi, I need to introduce new atomtypes/parameters and restrains in Gromacs for Fe3+. Could you please inform me on how can I do it? Thanks. Cheers, Carla -- View this message in context: http://gromacs.5086.n6.nabble.com/parameters-and-restrains-for-Fe3-tp4981309.html Sent from the GROMACS

[gmx-users] my e-mail to post in this list

my e-mail to post in this list is : carla.carluc...@libero.it -- 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_Lists/Search before posting! Please don't post (un)subscribe

Re: [gmx-users] about trifloroehanol

Thank you Justin .. I will follow your Instructions .. With Best Wishes, R.David -- 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_Lists/Search before posting! Please don't

[gmx-users] topology file in DPPC

Dear all, I'm meticulously following the tutorial KALP-15 in DPPC in order to carry on the simulation of a protein of mine in a extended patch of DPPC. I have already modified the ffnonbonded.itp and ffbonded.itp. At this point I'm reading that I should change my topology file but I'm not able to

Re: [gmx-users] topology file in DPPC

Do you know where I should look to find the solution to my problem? Silvia On 5/15/12 10:47 AM, scapr...@uniroma3.it wrote: Dear all, I'm meticulously following the tutorial KALP-15 in DPPC in order to carry on the simulation of a protein of mine in a extended patch of DPPC. I have

Re: [gmx-users] topology file in DPPC

On 5/15/12 11:11 AM, scapr...@uniroma3.it wrote: Do you know where I should look to find the solution to my problem? The entire procedure for modifying the force field is different, as the directory structure and file names are very different. The best solution is to upgrade your

Re: [gmx-users] about trifloroehanol

Thank you justin.. I will try to adhere spacing -- 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_Lists/Search before posting! Please don't post (un)subscribe requests to

Re: [gmx-users] Two [ dihedrals ] sections in topology

Hi You wrote: Two blocks of dihedrals are normal output for pdb2gmx - one for proper and one for improper dihedrals. Is there a way to force pdb2gmx that there is only my block with improper dihedrals in the topology? Could that be a problem in further calculations, i.e. energy

Re: [gmx-users] about trifloroehanol

On 5/15/12 8:25 AM, rama david wrote: Hi all Very sorry for my stupid question .. I really work a lot on these problem I wish to use Trifluroethanol as solvent for my study ... I Check the top file for G96 53a6 ff It shows TFE with following lines ... [ TFE ] [ atoms ] HT

[gmx-users] NVT conserved-energy lysozyme

Dear all I have been following Justin Lemkul's tutorial for the lysozyme simulations http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html I am using Gromacs 4.5.5. My concern is with the energy conservation in the implementation of Bussi's velocity-rescaling

Re: [gmx-users] ATB SWISSPARAM Topologies

Thanks a lot Justin! On Tue, May 15, 2012 at 4:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/15/12 5:54 AM, Anirban wrote: Hi ALL, How accurate are the topologies of non-standard molecules generated by ATB or SWISSPARAM for GROMACS? Are they acceptable for publications? Are we

[gmx-users] Problem in visualizing protein-ion complex trajectory in vmd

Dear gromacs users, I am running steered MD simulation using Plumed plugin in gromacs for a system consisting of Protein-Mg-GTP complex. I have to calculate the distance of specific atoms with Mg and GTP. While visualizing the trajectories using vmd, I am encountering some problems. 1) While

Re: [gmx-users] NVT conserved-energy lysozyme

On Tue, 2012-05-15 at 09:17 +0100, David de Sancho wrote: Dear all I have been following Justin Lemkul's tutorial for the lysozyme simulations http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html I am using Gromacs 4.5.5. Compiled in double or single

Re: [gmx-users] Generating_tpr_file from.xtc

Hi Shahid, You probably have a matching .top file lying around? You can use it with the .gro file to regenerate the .tpr. Note that most analysis can also be run with a .gro/.pdb file. Cheers, Tsjerk On Tue, May 15, 2012 at 4:30 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/15/12 10:28

Re: [gmx-users] Generating_tpr_file from.xtc

On 5/15/12 10:28 AM, shahid nayeem wrote: Dear users By mistake I have deleted my .tpr file after running simulation. Is it possible to generate .tpr file from .xtc .gro .log and .ene file of final production run. No. None of those files have the required topology information. -Justin --

Re: [gmx-users] Test Particle Insertion

Hi Steven. 1. Why this value is divided by nm3? Shall I multiply it by the simulation box? It is not not divided by nm3. The legend for y axis is not appropriate for your plot. Keep in mind that the same graph is used to represent lots of quantities (you can plot all of them with xmgrace -nxy

Re: [gmx-users] about the frame selection

On Tue, May 15, 2012 at 11:26 AM, rama david ramadavidgr...@gmail.comwrote: Hi Gromacs Users , I simulated a 4 peptide in a box . After completion of 30 ns simulattion , I extract the particular time frame 29000 ps of my interest. Now I want these frame for my next simulations study

[gmx-users] about trifloroehanol

Hi all Very sorry for my stupid question .. I really work a lot on these problem I wish to use Trifluroethanol as solvent for my study ... I Check the top file for G96 53a6 ff It shows TFE with following lines ... [ TFE ] [ atoms ] HT H 0.41000 0 OT OTFE-0.62500

Re: [gmx-users] about trifloroehanol

On 5/15/12 9:54 AM, rama david wrote: Hi to all Sorry Justin , I try to correct spacing but now it stuck to another problem pdb to TFE is as follow OMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 ATOM 1 CT TFE 1 -5.510 2.534 0.093 1.00 0.00 C ATOM

[gmx-users] DNA persistence length with g_polystat

Dear Gromacs users, I am doing MD simulation of DNA oligomers and need to calculate their persistence length. Using g_polystat with -p persist.xvg I discovered that the output file contains a lot of nan values among other values of numbers of bonds. As far as I understood reading this forum,

Re: [gmx-users] about trifloroehanol

Hi to all Sorry Justin , I try to correct spacing but now it stuck to another problem pdb to TFE is as follow OMPNDUNNAMED AUTHORGENERATED BY OPEN BABEL 2.3.0 ATOM 1 CT TFE 1 -5.510 2.534 0.093 1.00 0.00 C ATOM 2 CH2T TFE 1 -6.061 1.111

Re: [gmx-users] about the frame selection

On Tue, May 15, 2012 at 11:59 AM, Anirban reach.anirban.gh...@gmail.comwrote: Thank you Anirban I proceed as you mentioned... -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] How to calculate the center of the mass in gromacs

Is there the simple method to calculate the center of the mass for a group of atoms? I want to post-process the traj date file. Thanks a lot. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

[gmx-users] Generating_tpr_file from.xtc

Dear users By mistake I have deleted my .tpr file after running simulation. Is it possible to generate .tpr file from .xtc .gro .log and .ene file of final production run. shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] about the frame selection

Thank you ANIRBAN for your reply .. I think its better to remove the periodicity when you are going to start a fresh simulation with this protein. Could you told me how to remove the periodicity ??? Thank you in advance ... -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Test Particle Insertion

On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/14/12 11:53 AM, Steven Neumann wrote: Dear Gmx Users, Did anyone use TPI method for the calculation of chemical potential? The tpi.xvg files consists of: @ s0 legend -kT log(Ve\S-\xb\f{}U\N/V) @ s1 legend f.

Re: [gmx-users] about the frame selection

On Tue, May 15, 2012 at 11:48 AM, rama david ramadavidgr...@gmail.comwrote: Thank you ANIRBAN for your reply .. I think its better to remove the periodicity when you are going to start a fresh simulation with this protein. Could you told me how to remove the periodicity ??? You can use

[gmx-users] Re: NVT conserved-energy lysozyme

Thanks Florian and Mark for your replies. I have run the simulation for longer (one order of magnitude longer, i.e. 1 ns) and what I get now is that the 'conserved energy' follows its drift linearly. Now, of course, we are speaking about 1.2% drift/ns in the value of the energy, which seems quite

[gmx-users] ATB SWISSPARAM Topologies

Hi ALL, How accurate are the topologies of non-standard molecules generated by ATB or SWISSPARAM for GROMACS? Are they acceptable for publications? Are we required to carry out manual checks like that required for PRODRG outputs? Any suggestion is welcome. Thanks and regards, Anirban --

Re: [gmx-users] Problem in visualizing protein-ion complex trajectory in vmd

On 15/05/2012 10:22 PM, neeru sharma wrote: Dear gromacs users, I am running steered MD simulation using Plumed plugin in gromacs for a system consisting of Protein-Mg-GTP complex. I have to calculate the distance of specific atoms with Mg and GTP. While visualizing the trajectories using

[gmx-users] about the frame selection

Hi Gromacs Users , I simulated a 4 peptide in a box . After completion of 30 ns simulattion , I extract the particular time frame 29000 ps of my interest. Now I want these frame for my next simulations study .. In one simulation I want to keep the box size same as the mentioned in

Re: [gmx-users] Two [ dihedrals ] sections in topology

On 15/05/2012 8:47 PM, Lara Bunte wrote: Hi After pdb2gmx I have two [ dihedrals ] sections in my topology. The first block is empty, the second block is correct with my parameters. An an example: First block: [ dihedrals ] ; aiajakal functc0c1

[gmx-users] itp file for flavins

Does anyone have itp files for oxidized, reduced and semiquinone states of FMN (flavin mononucleotide)? I noticed gromacs is supposed to have rtp files for flavins, not sure how to access that. Thanks Vijaya Date: Tue, 15 May 2012 08:50:35 -0700 From: daviddesan...@gmail.com To:

[gmx-users] Two [ dihedrals ] sections in topology

Hi After pdb2gmx I have two [ dihedrals ] sections in my topology. The first block is empty, the second block is correct with my parameters. An an example: First block: [ dihedrals ] ;  ai    aj    ak    al funct    c0    c1    c2    c3    c4

[gmx-users] TFE Proper Dihedral types...

Hi Gromacs Friends .. I am using TFE (Trifluro Ethanol ) as a solvent for my simulation study.. I am using G96 53a6 ff After the genbox -cp .. -cs tef.pdb -o mix.pdb I count the no of solvent molecule , to update topology .. after Grompp I am facing following error grompp -f minim.mdp -c

Re: [gmx-users] ATB SWISSPARAM Topologies

On 5/15/12 5:54 AM, Anirban wrote: Hi ALL, How accurate are the topologies of non-standard molecules generated by ATB or SWISSPARAM for GROMACS? Are they acceptable for publications? Are we required to carry out manual checks like that required for PRODRG outputs? Any suggestion is welcome.

Re: [gmx-users] How to calculate the center of the mass in gromacs

On 5/15/12 11:35 AM, xu zhijun wrote: Is there the simple method to calculate the center of the mass for a group of atoms? I want to post-process the traj date file. This is a function of g_traj. -Justin -- Justin A. Lemkul, Ph.D. Department of

Re: [gmx-users] itp file for flavins

Please do not reply to an existing thread to ask a new question; start a new thread instead. On 5/15/12 12:03 PM, vijaya subramanian wrote: Does anyone have itp files for oxidized, reduced and semiquinone states of FMN (flavin mononucleotide)? I noticed gromacs is supposed to have rtp files

Re: [gmx-users] TFE Proper Dihedral types...

On 5/15/12 12:14 PM, rama david wrote: Hi Gromacs Friends .. I am using TFE (Trifluro Ethanol ) as a solvent for my simulation study.. I am using G96 53a6 ff After the genbox -cp .. -cs tef.pdb -o mix.pdb I count the no of solvent molecule , to update topology .. after Grompp I am facing

Re: [gmx-users] How to calculate the center of the mass in gromacs

Thanks a lot, Justin. It works well. Jerry --- On Tue, 5/15/12, Justin A. Lemkul jalem...@vt.edu wrote: From: Justin A. Lemkul jalem...@vt.edu Subject: Re: [gmx-users] How to calculate the center of the mass in gromacs To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Tuesday,

[gmx-users] Questions about Thermostats

Hello To make better energy minimization procedures I read about thermostats and barostats. I understand the physical concepts and differences between global and local thermostats and the difference between Berendsen and Nose-Hoover thermostat. 1.) Maybe this question is a little bit

Re: [gmx-users] Two [ dihedrals ] sections in topology

Hi Is there some reason to believe you should not have dihedrals?  That doesn't make much physical sense. I want and have dihedrals in my topology. I don't want an additional empty dihedrals block in the topology. In my force field I gave impropers. Greetings - Ursprüngliche

[gmx-users] Measure angle with g_sgangle

Hey. I'm using Gromacs to simulate a transmembrane-peptide and would like to measure the angle between three residues of the protein. The protein gets during the simulation a kink of about 87°. I would like to measure the real angle of the kink with g_sgangle. So I made an index file and

Re: [gmx-users] Measure angle with g_sgangle

On 5/15/12 2:47 PM, Mast, Thilo wrote: Hey. I'm using Gromacs to simulate a transmembrane-peptide and would like to measure the angle between three residues of the protein. The protein gets during the simulation a kink of about 87°. I would like to measure the real angle of the kink with

Re: [gmx-users] Two [ dihedrals ] sections in topology

On 5/15/12 2:53 PM, Lara Bunte wrote: Hi Is there some reason to believe you should not have dihedrals? That doesn't make much physical sense. I want and have dihedrals in my topology. I don't want an additional empty dihedrals block in the topology. In my force field I gave impropers.

Re: [gmx-users] itp file for flavins

On 5/15/12 5:37 PM, vijaya subramanian wrote: Hi I found all the rtp files-aminoacid.rtp,dna.rtp but not fmnr.rtp which is in ffgmx.rtp according to the gromacs building blocks site. I need to look at the fmnr.rtp file to match atom names. Individual molecules generally do not have their own

Re: [gmx-users] Two [ dihedrals ] sections in topology

On 16/05/2012 4:53 AM, Lara Bunte wrote: Hi Is there some reason to believe you should not have dihedrals? That doesn't make much physical sense. I want and have dihedrals in my topology. I don't want an additional empty dihedrals block in the topology. In my force field I gave impropers.

[gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks.

Hi, everyone. It is my first use of Gromacs and I am looking for a numerical scheme for one specific constrained SDE, the constrain is a macroscopic one, i.e., overdamped Langevin(Brownian dynamics) equations with an equality constraint which is expressed in form of expectation(or

Re: [gmx-users] TFE Proper Dihedral types...

On Tue, May 15, 2012 at 10:24 PM, Justin A. Lemkul jalem...@vt.edu wrote: The parameters are missing from ffbonded.itp, making the implementation incomplete. You can obtain a TFE topology from ATB:

[gmx-users] Coupling groups in protein-ligand-lipid simulation

Hi ALL, I am simulating a membrane protein docked with a ligand and embedded in a lipid bilayer. For COM removal I am using two groups, Prt_Lig_Lipid and SOL_CL. For temperature and pressure couplings should I use these two groups or should I use three groups, Protein, Lipid and Lig_SOL_CL? Any

[gmx-users] How can i specify a user defined potential between i, i+2 residues

Hi all, I use a user defined potential to describe non-bonded interactions, as this excludes i, i+2,i+3. If i want to describe a user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give that in mdp file. T -- gmx-users mailing list

[gmx-users] Fwd: How can i specify a user defined potential between i, i+2 residues

Hi all, I use a user defined potential to describe non-bonded interactions, as this excludes i, i+2,i+3. If i want to describe a user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give that in mdp file. Thanks for a reply in

Re: [gmx-users] How can i specify a user defined potential between i, i+2 residues

On 16/05/2012 3:43 PM, mohan maruthi sena wrote: Hi all, I use a user defined potential to describe non-bonded interactions, as this excludes i, i+2,i+3. If i want to describe a user defined potential for i,i+2,i+3,(i.e, 1-2,1-3) residues , how can i give that in mdp file. Doing

Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks.

On 16/05/2012 12:28 PM, kevin wrote: Hi, everyone. It is my first use of Gromacs http://lammps.sandia.gov/ and I am looking for a numerical scheme for one specific constrained SDE, the constrain is a macroscopic one, i.e., overdamped Langevin(Brownian dynamics) equations with an equality