[gmx-users] How could I know whether I should use epsilon-sigma or c6-c12?

Hi, Mark, The values of c6-c12 parameters are different from the values of epsilon and sigma, and they can be converted to each other. My point is which values I should specify in my .top file. Or it does not matter totally and Gromacs will determine what kinds of values you are specifying. Tha

Re: [gmx-users] How could I know whether I should use epsilon-sigma or c6-c12?

On 5/06/2012 5:04 PM, Bao Kai wrote: Hi, Mark, The values of c6-c12 parameters are different from the values of epsilon and sigma, and they can be converted to each other. My point is which values I should specify in my .top file. Or it does not matter totally and Gromacs will determine what k

[gmx-users] trajectory analysis

Hi all, I would like to get information about *pi-pi stacking*, *van der Waals*, *electrostatic and hydrophobic interactions* for my system (several-peptides in a box filled with water). Can Gromacs compute these interactions? As far as I see from mailing-list, to get information on *hydrophobi

Re: [gmx-users] Electrostatic interactions and atoms with nul charge

Hello, Thank you very much for your reply. I actually carried out very basic MDs of a peptide in vacuum (no pbc, cut-off for electrostatics and vdw = "infinity", niter = 10^6). The computing results are given in the two tables below. As they are identical, I am assuming that there is only o

Re: [gmx-users] Electrostatic interactions and atoms with nul charge

On 5/06/2012 6:46 PM, Laurence Leherte wrote: Hello, Thank you very much for your reply. I actually carried out very basic MDs of a peptide in vacuum (no pbc, cut-off for electrostatics and vdw = "infinity", niter = 10^6). The computing results are given in the two tables below. As they are

[gmx-users] Dispersion Corrections

I have read the section about Dispersion Correction in the manual 4.5.4 and there is no reference on how it is implemented. I am most interested on how this correction affects the surface tension. Can anybody tell me the reference of the paper and how dispersion corrections influence on surface te

Re: [gmx-users] trajectory analysis

On 6/5/12 4:40 AM, Turgay Cakmak wrote: Hi all, I would like to get information about *pi-pi stacking*, *van der Waals*, *electrostatic and hydrophobic interactions* for my system (several-peptides in a box filled with water). Can Gromacs compute these interactions? As far as I see from ma

Re: [gmx-users] trajectory analysis

Thank you for your reply. I will read the manual more carefully. 2012/6/5 Justin A. Lemkul > > > On 6/5/12 4:40 AM, Turgay Cakmak wrote: > >> >> Hi all, >> >> >> I would like to get information about *pi-pi stacking*, *van der Waals*, >> *electrostatic and hydrophobic interactions* for my system

Re: [gmx-users] Steered MD

You mean TMD (Targeted Molecular Dynamics). As far as I know, this is not implemented in GROMACS (hope anyone corrects me if I am wrong) 2012/6/4 Mike M > Dear Gromacs Users, > > I am trying to study the conformational path from state A to state B with > targeted molecular dynamics. These two

Re: [gmx-users] Steered MD

Take a look at this post: http://lists.gromacs.org/pipermail/gmx-users/2002-November/003378.html 2012/6/5 Miguel Ángel Mompeán García > You mean TMD (Targeted Molecular Dynamics). As far as I know, this is not > implemented in GROMACS (hope anyone corrects me if I am wrong) > > > > 2012/6/4

Re: [gmx-users] Writing and compiling new analyses for gromacs

Thanks I'll try that 2012/6/5 Peter C. Lai > The quick and dirty way is to post-patch Makefile in src/tools. > > I think patching the appropriate Makefile.in is sufficient for configure to > pick up and automake into Makefile if all you need to do is append a make > target. > > As to your previo

Re: [gmx-users] Writing and compiling new analyses for gromacs

2012/6/5 Mark Abraham > On 5/06/2012 9:11 AM, Peter C. Lai wrote: > >> The quick and dirty way is to post-patch Makefile in src/tools. >> >> I think patching the appropriate Makefile.in is sufficient for configure >> to >> pick up and automake into Makefile if all you need to do is append a make

Re: [gmx-users] Writing and compiling new analyses for gromacs

5 jun 2012 kl. 14.23 skrev Shay Teaching: > > > 2012/6/5 Mark Abraham > On 5/06/2012 9:11 AM, Peter C. Lai wrote: > The quick and dirty way is to post-patch Makefile in src/tools. > > I think patching the appropriate Makefile.in is sufficient for configure to > pick up and automake into Makef

[gmx-users] What does this message mean?

Hi, all, It is very easy for me to get the following message. WARNING: nmol = 1, this may not be what you want. Temperature dependent fluctuation properties at T = 317.98. I am wondering if somebody can tell me what does it mean or if it is a problem to improve? Thank you very much. Best Rega

[gmx-users] Trajectories

I am interested in pulling out the trajectories (x,y,z coordinates) of water molecules within a certain distance of my solute molecule. I have tried using g_select, but that will only give me the atom numbers and not the trajectories. I can create an index file using this command but unfortunatel

Re: [gmx-users] Trajectories

On 6/5/12 9:02 AM, rankinb wrote: I am interested in pulling out the trajectories (x,y,z coordinates) of water molecules within a certain distance of my solute molecule. I have tried using g_select, but that will only give me the atom numbers and not the trajectories. I can create an index fi

Re: [gmx-users] Writing and compiling new analyses for gromacs

2012/6/5 Erik Marklund > > 5 jun 2012 kl. 14.23 skrev Shay Teaching: > > > > 2012/6/5 Mark Abraham > >> On 5/06/2012 9:11 AM, Peter C. Lai wrote: >> >>> The quick and dirty way is to post-patch Makefile in src/tools. >>> >>> I think patching the appropriate Makefile.in is sufficient for configur

Re: [gmx-users] What does this message mean?

On 5/06/2012 10:51 PM, Bao Kai wrote: Hi, all, It is very easy for me to get the following message. WARNING: nmol = 1, this may not be what you want. Temperature dependent fluctuation properties at T = 317.98. I am wondering if somebody can tell me what does it mean or if it is a problem to i

Re: [gmx-users] Trajectories

5 jun 2012 kl. 15.05 skrev Justin A. Lemkul: > > > On 6/5/12 9:02 AM, rankinb wrote: >> I am interested in pulling out the trajectories (x,y,z coordinates) of water >> molecules within a certain distance of my solute molecule. I have tried >> using g_select, but that will only give me the atom

[gmx-users] tip5p tip, not good, energy can only get -39, not -45

HI All, I run the tip5p water model, i found the computed properties are not good, e.g. energy. Can anyone know the problem? i need to get the surface potential, it can get -1 V regards -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Plea

[gmx-users] Re:What does this message mean?

Hi, Mark, Following please find the information. pure_water]$ g_energy_d -f step11.edr :-) G R O M A C S (-: GROwing Monsters And Cloning Shrimps :-) VERSION 4.5.5 (-: Written by Emile Apol, Rossen Apo

Re: [gmx-users] Trajectories

Dear Rankinib, You can do it with a 5 line bash script as well, cat everything times x,y,z and just cut and past them into a spread sheet, and save it with tabs or spaces. Stephan Watkins Original-Nachricht > Datum: Tue, 05 Jun 2012 09:05:09 -0400 > Von: "Justin A. Lemkul" >

Re: [gmx-users] Trajectories

Original-Nachricht > Datum: Tue, 05 Jun 2012 09:05:09 -0400 > Von: "Justin A. Lemkul" > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] Trajectories > > > On 6/5/12 9:02 AM, rankinb wrote: > > I am interested in pulling out the trajectories (x,y,z coordinate

Re: [gmx-users] Trajectories

Hi, I think Erik meant to say that the program is trjorder (not g_order) for the ordering of molecules by distance. Cheers Tom On 05/06/12 14:41, Erik Marklund wrote: 5 jun 2012 kl. 15.05 skrev Justin A. Lemkul: On 6/5/12 9:02 AM, rankinb wrote: I am interested in pulling out the traje

RE: [gmx-users] Trajectories

Thank you all for your replies. Stephan -- can you explain a little more about your 5 line bash script idea? The only part I am not sure about is pulling out the water molecules within a certain distance. Are you suggesting to write a script that calculates atom distance and saves only those

[gmx-users] Selecting atom indices of residues whose centers of mass match a position range

Hi, I would like to use g_select_d to generate an index file containing the atoms of BF4 residues whose centers of mass are in the range z<12.24 nm. I have tried the following: g_select -f traj.xtc -s topol.tpr -select 'resname BF4 and res_com and z<12.24' -on output.ndx But the selection synt

Re: [gmx-users] Trajectories

You can also use something like VMD where you load the trajectory then select your atoms, then increment the frames and extract the xyz coordinates of each of your atoms in the selection. You can do that in 5 lines of TCL script (just don't update the select within selection after each frame or el

Re: [gmx-users] Selecting atom indices of residues whose centers of mass match a position range

On 6/5/12 2:55 PM, Andrew DeYoung wrote: Hi, I would like to use g_select_d to generate an index file containing the atoms of BF4 residues whose centers of mass are in the range z<12.24 nm. I have tried the following: g_select -f traj.xtc -s topol.tpr -select 'resname BF4 and res_com and z<1

[gmx-users] How to add DMSO as solvent?

Hello all, Assuming that I made my own .itp file for amber99sb-compatible DMSO parameters (based on Thomas Fox and Peter A. Kollman. J. Phys. Chem. B., 1998, 102, 8070-8079) and included that in the .top file, how can I add DMSO to my system? Should I also make a .gro file in analogy to spc216.gro

Re: [gmx-users] How to add DMSO as solvent?

There are a number of programs that will let you build coordinates of molecules: PRODRG, ArgusLab, VMD etc. You'll have to make sure the atom naming and order are correct with respect to your .itp. You'll probably have to reminimize the structure so the geometry fits the one specified by your FF/

Re: [gmx-users] How to add DMSO as solvent?

On 6/5/12 6:03 PM, Yun Shi wrote: Hello all, Assuming that I made my own .itp file for amber99sb-compatible DMSO parameters (based on Thomas Fox and Peter A. Kollman. J. Phys. Chem. B., 1998, 102, 8070-8079) and included that in the .top file, how can I add DMSO to my system? Should I also mak

[gmx-users] chirality changes during the simulation

Dear GMX users, I have some trajectories of Ala-Ala dipepetides with COOH terminals (Cap-Ala-Ala-COOH), However, I saw the chirality of the Ala-COOH doesn't maintained as L form during the simulation, there are D-forms, is it because there are some lacks of parameters of this part or Gromacs doesn

[gmx-users] "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" error during minimization with TPO residue

I am trying to simulate a system with a phosphorylated threonine residue using Gromacs 4.5.5. I took the parameters for the TPO residue from the gromos43a1p force field and added them to the gromos43a1 force field, following the steps as provided on the Gromacs website. I then successfully complete

Re: [gmx-users] "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" error during minimization with TPO residue

On 6/5/12 7:36 PM, Alex Cumberworth wrote: I am trying to simulate a system with a phosphorylated threonine residue using Gromacs 4.5.5. I took the parameters for the TPO residue from the gromos43a1p force field and added them to the gromos43a1 force field, following the steps as provided on th

[gmx-users] TIP3P or TIP4P

Hi! I want to perform a simulation with TIP4P water model. I want to know this simulation how much slower than TIP3P water model or spc216 model approximately? number of solvent molecules in my system are about 2500. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mail

Re: [gmx-users] "X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" error during minimization with TPO residue

I apologize to anyone who wasted their time reading my original post: I found that integrator had been misspelt in the em.mdp file, causing it to default to integrator = md. After fixing the mistake, no more errors resulted. Alex On Tue, Jun 5, 2012 at 4:46 PM, Justin A. Lemkul wrote: > > > On

Re: [gmx-users] chirality changes during the simulation

On 6/06/2012 8:31 AM, mu xiaojia wrote: Dear GMX users, I have some trajectories of Ala-Ala dipepetides with COOH terminals (Cap-Ala-Ala-COOH), However, I saw the chirality of the Ala-COOH doesn't maintained as L form during the simulation, there are D-forms, is it because there are some lack

Re: [gmx-users] TIP3P or TIP4P

On 6/06/2012 10:33 AM, Amir Abbasi wrote: Hi! I want to perform a simulation with TIP4P water model. I want to know this simulation how much slower than TIP3P water model or spc216 model approximately? number of solvent molecules in my system are about 2500. Do a 5 minute test on each and se

Re: [gmx-users] comparing simulations with diffrent forcefields

Dear Justin,   Thank you very much for the reply   Sogol From: Justin A. Lemkul To: Kowsar Bagherzadeh ; Discussion list for GROMACS users Sent: Monday, May 28, 2012 6:06 PM Subject: Re: [gmx-users] comparing simulations with diffrent forcefields On 5/28/12

[gmx-users] Regarding error

Dear all gromacs users, While i am running pdb2gmx commond i am getting following error. Fatal error: incomplete ring in HIS231 Kindly tell me how to overcome this error and how to

Re: [gmx-users] Re:What does this message mean?

On 6/06/2012 12:26 AM, Bao Kai wrote: Hi, Mark, Following please find the information. pure_water]$ g_energy_d -f step11.edr :-) G R O M A C S (-: GROwing Monsters And Cloning Shrimps :-) VERSION 4.5.5 (-:

Re: [gmx-users] tip5p tip, not good, energy can only get -39, not -45

On 5/06/2012 11:47 PM, MD wrote: HI All, I run the tip5p water model, i found the computed properties are not good, e.g. energy. Probably you haven't run it well enough or long enough. Can anyone know the problem? i need to get the surface potential, it can get -1 V Not unless they are ab

[gmx-users] Regarding error.

Dear all gromacs users, I have 1VZV.pdb file, in that file HIS231 has incomplete ring as N atom is missing.Can i add N atom to the .pdb file if possible how can i add that atom to .pdb file. Suryanarayana Seera, PhD student, India. -- gmx-users mailing listg

Re: [gmx-users] Regarding error.

There is no GROMACS tool that repairs incomplete structures, but you can find other programs that can do it. Some of them have been previously posted in this list (try a search on it). Personally I've used Swiss PDB viewer, which is useful to add missing atoms. Javier El 06/06/12 07:42, Seera