[gmx-users] Gromacs Building Blocks

Hello I read about Gromacs building blocks ( http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks ) and there is written following table. How to do a MD Smiluation with this building blocks? Greetings Abbrev. Source 2 Full Name FAD ffgmx.rtp O flavin adenine dinucleot

[gmx-users] MD in Vacuum

Hello In all my tutorials for md they investigate a molecule in solution. I want to do md simulations in vacuum and I did not find a good tutorial. So I want to ask you what should I do for a md simulation in vaccum? I take a molecule, optimize the structure, generate a topology with gromacs an

[gmx-users] mails of other users in this mailing list

Hello Is there a way to get all mails from the GROMACS mailing list for a special email adress? To be more precisely I want to have all messages that are asked and answered for a special user. This is motivated out of the fact that I saw that I am not alone with my system. There are other peo

Re: [gmx-users] Water molecule can not be settled - mdrun error

simulations collapse, then the parameterization is likely insufficiently accurate. -Justin > On 2012-09-24 05:07:59PM +0100, Lara Bunte wrote: >> Hi >> >> The result of the energy minimization before is: >> >> Steepest Descents: >>    Tolerance (Fmax)  =  1.

Re: [gmx-users] Water molecule can not be settled - mdrun error

. Lai An: Discussion list for GROMACS users CC: Lara Bunte Gesendet: 22:13 Freitag, 21.September 2012 Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error On 2012-09-21 02:59:17PM -0400, Justin Lemkul wrote: > > > On 9/21/12 1:31 PM, Lara Bunte wrote: > > Hi J

Re: [gmx-users] Water molecule can not be settled - mdrun error

SO SOL   > tau_t   = 0.1   0.1 > ref_t   = 300   300 > > pcoupl  = no I am totaly frustrated and shortly for giving it up :-(:-( :-( Best greetings Lara - Ursprüngliche Message - Von: Peter C. Lai An: Lara Bunte CC: "gmx-users@grom

Re: [gmx-users] About mdrun -nt number

If I have 24 processors in the machine, I could use mdrun -nt 24 for a high performance? Greetings Lara - Ursprüngliche Message - Von: Peter C. Lai An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 17:58 Montag, 24.September 2012 Betreff: Re: [gmx-users] About

Re: [gmx-users] About mdrun -nt number

un threads -nt N is used to basically tell mdrun how many threads to spawn on the local host. We refer to threads since on some architectures, a single core can handle multiple threads. (like 2 threads per core with hyperthreading). On 2012-09-24 04:33:19PM +0100, Lara Bunte wrote: > Hi > &

Re: [gmx-users] Water molecule can not be settled - mdrun error

  = V-rescale tc-grps = ISO SOL   tau_t   = 0.1   0.1 ref_t   = 300   300 pcoupl  = no Greetings Lara - Ursprüngliche Message - Von: Peter C. Lai An: Lara Bunte CC: "gmx-users@gromacs.org" Gesendet: 17:46 Montag, 24

[gmx-users] Meaning of Table Size

Hello What exactly is the table size? grompp gives me this warnin: Warning: 1-4 interaction between 1 and 5 at distance 2.751 which is larger than the 1-4 table size 2.500 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase

[gmx-users] About mdrun -nt number

Hi In the man page of mdrun is written for the option -nt int: "Number of threads to start (0 is guess)" What do this mean? What is a thread in this context? Thanks Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please se

Re: [gmx-users] Water molecule can not be settled - mdrun error

tings Lara - Ursprüngliche Message - Von: Justin Lemkul An: Discussion list for GROMACS users CC: Gesendet: 17:33 Freitag, 21.September 2012 Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error On 9/21/12 11:26 AM, Lara Bunte wrote: > Hi Justin > > Sor

Re: [gmx-users] Water molecule can not be settled - mdrun error

settings? Greetings Lara - Ursprüngliche Message - Von: Justin Lemkul An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 16:04 Freitag, 21.September 2012 Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error On 9/21/12 9:45 AM, Lara Bunte w

[gmx-users] Water molecule can not be settled - mdrun error

Hello My equilibration of water around lumiflavin works (I got no error, no warning and no note). Sadly the mdrun fails with following error: step 886: Water molecule starting at atom 7596 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. What does GROMACS me

[gmx-users] CHARMM27 Equilibrating Settings

Hello In my former questions I got some answers that leads me to following question (I am really thankful for that. This mailing list and the people here are great :-) ). I am using a CHARMM27 force field and it seems that I often used wrong settings in equilibrating and energy minimization. So

[gmx-users] Problems in mdrun - CHARMM27

Hello Could you please take a look on my new pr.mdp file that I created for equilibrating water around lumiflavin. grompp works but I guess there must be something wrong because after grompp I am using mdrun and get this warning: Warning: 1-4 interaction between 1 and 5 at distance 2.429 which

[gmx-users] Theoretical questions about cut-offs and neighbor searching

Hello In my practice calculation I made wrong cut-offs in an energy minimization. After the help of Justin and Peter (thanks a lot) it works and now I have some theoretical question about this. I read about cut-offs in the manual but I don't understand it really. Could you please explain me

[gmx-users] Equilibration Water around Alanin - Problem with Names

Hello I want to equilibrate water around the amino acid alanin. I guess I have no further errors up to here. In my pdb file of alanin stands in the first line COMPND Alanin In my topology in the [ moleculetype ] block stands at name: Protein_chain_A. At the end of the topology file stands in

Re: [gmx-users] Energy Minimization of Alanin

, Lara Bunte wrote: > Hello > > I want to do md simulations with the amino acid alanin for practice. I choose > alanin because it is parametrized in my forcefield. I use charmm27. > > I created with pdb2gmx my topology and I use water model tip3p. I choosed a > dodecahedron box

[gmx-users] Energy Minimization of Alanin

Hello I want to do md simulations with the amino acid alanin for practice. I choose alanin because it is parametrized in my forcefield. I use charmm27. I created with pdb2gmx my topology and I use water model tip3p. I choosed a dodecahedron box with distance of 0.5 between the solute and this b

Re: [gmx-users] PDB and XYZ Structure Files in GROMACS

Hi Justin I really forgot this old mail. I am sorry for that. editconf worked :) Greetings Lara - Ursprüngliche Message - Von: Justin Lemkul An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 16:04 Dienstag, 18.September 2012 Betreff: Re: [gmx-users] PDB and XYZ

[gmx-users] PDB and XYZ Structure Files in GROMACS

Hello Is it possible with GROMACS to convert a given .pdb structure file to a .xyz structure file? Thanks for help Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Suppo

Re: [gmx-users] Structure optimization failure

same problem. The water could not be settled. What is wrong with this file for my system? Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 12:23 Freitag, 29.Juni 2012 Betreff: Re: [gmx-users] Structure

[gmx-users] Structure optimization failure

Hello I use a CHARMM27 force field and my system is lumiflavin in water. I use the spc216 water model, a dodecahedral box with 1.3 nm. I want to make a structure minimization. I made a file pr.mdp. Could you please tell me, what I could do better in this file, or what is wrong? I guess there ha

[gmx-users] pdb to xyz file format

Hi Is it possible to convert a .pdb file to a .xyz file with GROMACS? At this point there shouldn't be a force field or final topology, I just want to convert this formats to each other. Is it possible with GROMACS? Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lis

Re: [gmx-users] Configurational bias Monte Carlo

Hi >Monte Carlo methods in GROMACS 5.0. Thats cool, when will GROMACS 5.0 be released? Greetings Lara - Ursprüngliche Message - Von: Michael Shirts An: Discussion list for GROMACS users CC: Gesendet: 18:24 Freitag, 1.Juni 2012 Betreff: Re: [gmx-users] Configurational bias Mo

[gmx-users] unit conversion of a force constant

Hello If I have a force constant 287 kcal/(mol * A^2), the A stands for Angstrom and I want to calculate this to kJ/(mol * nm^2), is it correct that I have to multiply 4.19/0.01 = 419 to the force constant? Is ithis true:  287 kcal/(mol * A^2) = 120253 kJ/(mol * nm^2) Could this be a physica

[gmx-users] no pr.gro file for energy minimization

Hello After equilibrating the water around my molecule I want to run the MD simulation. In my tutorial this is primed with: grompp -f run.mdp -p topol.top -c pr.gro -o run.tpr I don't have this pr.gro file but I have a pr.tpr file. Could I use this one? It seems GROMACS accepts this but I don'

[gmx-users] Equilibrating Water around the Molecule

Hello I want to equilibrate the water around my molecule. For doing this I created a pr.mdp file that makes most sense for me. Sadly I am a beginner with less knowledge, so could you please take a look on this pr.mdp file and say me if this is good or if not, what would you suggest to me? My Sy

Re: [gmx-users] Force Constants and Unit Systems

That helps a lot. Thank you, I guess I got it now :-) Greetings Lara - Ursprüngliche Message - Von: Richard Broadbent An: Lara Bunte ; Discussion list for GROMACS users CC: "jalem...@vt.edu" Gesendet: 11:21 Freitag, 18.Mai 2012 Betreff: Re: [gmx-users] Force Constant

Re: [gmx-users] Force Constants and Unit Systems

ant is divided by mol. What is the reason for this? In example Energy/length^2 is the force constant, why do we consider Energy/(mol * lenght^2) ? Thanks for helping me Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Lara Bunte ; Discussion list for GROMACS user

Re: [gmx-users] Force Constants and Unit Systems

g=AFQjCNFOxi8Cf2eUshmA9rzPfLPra5u-gw&sig2=79QqmWk3b8LSFlVjey4FFg Do you think it is a typo? Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 20:37 Donnerstag, 17.Mai 2012 Betreff: Re: [gmx-users] Force Con

Re: [gmx-users] Force Constants and Unit Systems

that means probably, that the writers of the paper did an error. Could such an error ruin my hole MD? My complete force field parametrization is out of this paper. Thanks for helping me Greetings Lara - Ursprüngliche Message - Von: Richard Broadbent An: Lara Bunte ; Discussi

Re: [gmx-users] Force Constants and Unit Systems

trization I have this values. Could you please explain this? Greetings and really thanks for your help Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 18:52 Donnerstag, 17.Mai 2012 Betreff: Re: [gmx-users] For

[gmx-users] Force Constants and Unit Systems

Hello I never had contact with such units. Could you please help me and explain me how to transform following units:   1.) kcal / mol --> kJ / (mol * nm^2) 2.) kcal / (mol * rad^2) --> kJ / (mol * rad^2) I have additionally some question to that:  Both should be units of a force constant. From

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

- Von: Justin A. Lemkul An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 17:02 Donnerstag, 17.Mai 2012 Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology On 5/17/12 10:48 AM, Lara Bunte wrote: > Hi > > grompp -f em.mdp -p topol.top -c solvated.gro -o em.

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

f the topol.top file. Greetings Lara - Ursprüngliche Message - Von: Mark Abraham An: Discussion list for GROMACS users CC: Gesendet: 2:35 Mittwoch, 16.Mai 2012 Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology On 16/05/2012 4:53 AM, Lara Bunte wrote: > Hi > >&

[gmx-users] grompp error - incorrect number of parameters

Hello After grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr I got the error: Incorrect number of parameters - found 2, expected 4 or 4 for U-B. I thought that this could be an inconsistency be declaring the functions, but in my topology I have function 4 (for improper dihedrals)

Re: [gmx-users] grompp Unkown bond_atomtype C2

n A. Lemkul An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 13:22 Mittwoch, 16.Mai 2012 Betreff: Re: [gmx-users] grompp Unkown bond_atomtype C2 On 5/16/12 3:56 AM, Lara Bunte wrote: > Hi > > After: > > pdb2gmx -f mymol.pdb -water tip3p > editconf -f co

[gmx-users] grompp Unkown bond_atomtype C2

Hi After: pdb2gmx -f mymol.pdb -water tip3p  editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro I typed: grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr where em.mdp is my energy minimization file and I got: Fata

[gmx-users] pdb2gmx Warning: Long Bond

Hi If I use pdb2gmx -f mymol.pdb -water tip3p (CHARMM27 force field) I got warnings like this: Making bonds... Warning: Long Bond (1-2 = 0.261872 nm) Warning: Long Bond (2-4 = 0.267812 nm) Warning: Long Bond (6-4 = 0.260531 nm) and so on For what problem tries GROMACS to warn me? Should I

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

-- Ursprüngliche Message - Von: Justin A. Lemkul An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 17:02 Dienstag, 15.Mai 2012 Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology On 5/15/12 10:43 AM, Lara Bunte wrote: > Hi > > You wrote: > >>

[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 hairspl

[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

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

] for using CHARMM27 force field? Thanks Greetings Lara - Ursprüngliche Message - Von: Mark Abraham An: Discussion list for GROMACS users CC: Gesendet: 12:57 Dienstag, 15.Mai 2012 Betreff: Re: [gmx-users] Two [ dihedrals ] sections in topology On 15/05/2012 8:47 PM, Lara Bunt

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

ng me Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Discussion list for GROMACS users CC: Gesendet: 20:59 Montag, 7.Mai 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology On 5/7/12 2:54 PM, Lara Bunte wrote: > Hi > >

[gmx-users] Atom Types in ffbonded.itp

Hello I want to write my parameters in the ffbonded.itp file in the CHARMM27 force field folder. I wrote my atom types in this file. This atom types are defined by me in atomtypes.dat grompp gives me an error  Fatal error: Unknown bond_atomtype for all my atom types. Do I have to declare that

Re: [gmx-users] Atom Names or Atom Types in the force field paramerization

Hi Justin In my flamol.rtp file that I create in my force field order CHARMM27 Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 20:32 Montag, 14.Mai 2012 Betreff: Re: [gmx-users] Atom Names or Atom

[gmx-users] Atom Names or Atom Types in the force field paramerization

Hello I saw that in my force field parametrization I wrote the atom names and not the atom types in the blocks like bonds, angles and so on. Could this be a problem? Should I write the atom types in the blocks? Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.

[gmx-users] First Energy Minimization in a MD

Hello I read the mdp options more than once but I don't understand how to make a good em.mdp file for the first energy minimization, if you plug your molecule in a water box. In my tutorial is this example given. integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulom

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

ssage - Von: Justin A. Lemkul An: Discussion list for GROMACS users CC: Gesendet: 21:59 Sonntag, 6.Mai 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology On 5/6/12 3:45 PM, Lara Bunte wrote: > Hi > > You said: > >> The blank lines will be

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

etings Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Discussion list for GROMACS users CC: Gesendet: 20:34 Dienstag, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: > Hi > > In some lines the equili

[gmx-users] Automation of selecting water around a molecule

Hi I need a little help in using Linux. I wrote this script for the bash, that I called g_select_script.sh: #!/bin/bash g_select -s mol_in_water.pdb -select '"Close to ISO" resname SOL and within 0.4 of resname ISO' -on make_ndx -f mol_in_water.pdb -o index2.ndx cat index2.ndx index.ndx > ind

Re: [gmx-users] File editing - only one layer of water around a molecule

h "Close to ISO"? Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Discussion list for GROMACS users CC: Gesendet: 20:55 Dienstag, 1.Mai 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 5/1/12 2:40 PM, L

Re: [gmx-users] File editing - only one layer of water around a molecule

Hi There is a new problem :-( If I used the commands g_select -s molecule.pdb -select '"Close to ISO" resname SOL and within 1.2 of resname ISO' and trjconv -n index.ndx -f molecule.pdb -s molecule.pdb -o output.pdb I got only water in my output.pdb Than I tried all 8 possible permutations

[gmx-users] File editing - only one layer of water around a molecule (again)

Hello After I understand how to select a molecule with water layers out of a molecule in a box filled with water (again thanks to Justin and Mark for lots of help), I want to understand more about choosing good parameters in g_select. I have the command g_select -s molecule_in_water.pdb -

Re: [gmx-users] File editing - only one layer of water around a molecule

or being such patient with me. Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Discussion list for GROMACS users CC: Gesendet: 18:35 Montag, 30.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/30/12 12:29 PM, Lara Bunte wrote

Re: [gmx-users] File editing - only one layer of water around a molecule

helping me. Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Lara Bunte ; Discussion list for GROMACS users CC: Gesendet: 18:07 Montag, 30.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/30/12 11:41 AM, Lara Bunte wrote

[gmx-users] New Gromacs Release

Hi Just out of curiosity: When will be the next release for a new version of Gromacs with extended manual? Greetings Lara -- 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] File editing - only one layer of water around a molecule

üngliche Message - Von: Justin A. Lemkul An: Discussion list for GROMACS users CC: Gesendet: 19:44 Montag, 23.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/23/12 1:27 PM, Lara Bunte wrote: > Hi > > In this case my problem is

Re: [gmx-users] File editing - only one layer of water around a molecule

Hi In this case my problem is not solvable with gromacs? All I have is the my_molecule.pdb which is a small molecule in a water box and my generated index.ndx file, size.xvg file and output.xtc file. Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul An: Lara Bunte

Re: [gmx-users] File editing - only one layer of water around a molecule

.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/23/12 11:01 AM, Lara Bunte wrote: > Hi > > What do you mean with > > >> Specify a .pdb file as the output of your original command. > > I wrote in > > > tr

Re: [gmx-users] File editing - only one layer of water around a molecule

An: Discussion list for GROMACS users CC: Gesendet: 13:02 Montag, 23.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/23/12 3:46 AM, Lara Bunte wrote: > > > Hi > > that worked. I used > > trjconv -n index.ndx -f my_molecule.pdb -o o

Re: [gmx-users] File editing - only one layer of water around a molecule

l An: Discussion list for GROMACS users Gesendet: 23:10 Sonntag, 22.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/22/12 5:07 PM, Lara Bunte wrote: > Hi > > I got always the same error. I tried > > trjconv -n index.ndx -s molecule_in

Re: [gmx-users] File editing - only one layer of water around a molecule

s for helping Greetings Lara Von: Justin A. Lemkul An: Discussion list for GROMACS users Gesendet: 22:37 Sonntag, 22.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/22/12 3:55 PM, Lara Bunte wrote: > H

Re: [gmx-users] File editing - only one layer of water around a molecule

__ Von: Justin A. Lemkul An: Discussion list for GROMACS users Gesendet: 17:27 Samstag, 14.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule Lara Bunte wrote: > Hi Justin > > The difference in my > > g_select

Re: [gmx-users] File editing - only one layer of water around a molecule

Greetings Lara p.s. I use yahoo. I tried to find an "answer to all" option or something like that. Again after pressing answer the mail should go only to Justin. I put the mailing list in cc. Is here someone using yahoo also and know how to fix this?

[gmx-users] g_select tutorial

Hello I want and need a tutorial especially for g_select but I found nothing. Do you know a tutorial for g_select? Manual and help are here not enough to understand how to use g_select. Thanks Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g

Re: [gmx-users] File editing - only one layer of water around a molecule

Please help Greetings Lara Von: Teemu Murtola An: Discussion list for GROMACS users Gesendet: 18:20 Freitag, 13.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On Fri, Apr 13, 2012 at 18:30, Lara Bunte wrote: > Is there no way only to use the

Re: [gmx-users] File editing - only one layer of water around a molecule

[gmx-users] File editing - only one layer of water around a molecule Lara Bunte wrote: > Hi Justin > > Okay, after > > g_select -f mol_in_water.pdb -select '"Close to ISO" resname SOL and within > 0.5 of group "ISO"' > > I got: > >

Re: [gmx-users] File editing - only one layer of water around a molecule

cked. I don't get it. :-( Greetings Lara p.s. Here in this email if I got to answer (like always) is only Justins mail adress, not the gromacs user list. I do it in cc ____ Von: Justin A. Lemkul An: Lara Bunte ; Discussion list for GROMACS users Ges

Re: [gmx-users] File editing - only one layer of water around a molecule

users] File editing - only one layer of water around a molecule On 13/04/2012 8:17 PM, Lara Bunte wrote: Thanks for that but where in this do I give Gromacs my pdb. file. From where do g_select use this information? > > > >What I have is a pdb file. > Look at g_select -h fo

Re: [gmx-users] File editing - only one layer of water around a molecule

Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 13/04/2012 8:01 PM, Lara Bunte wrote: Hi Mark > > >Could you please give me for that the prompt how to write this in the console. > > > >"All atoms of a residue LIG within 0.5 nm o

Re: [gmx-users] Box Size in MD

Hi Justin What is a box vector? I read that the CHARMM force field that I am using has a cut-off of 1 (is this Angstrom or nano-meters?). So should I use a box size of 3 nano-meters? Greetings Lara Von: Justin A. Lemkul An: Lara Bunte ; Discussion list

Re: [gmx-users] File editing - only one layer of water around a molecule

Gesendet: 11:51 Freitag, 13.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 13/04/2012 7:29 PM, Lara Bunte wrote: I read g_select -select 'help all' and I understand nothing of that. > > > >In general one have a molecule (vale

Re: [gmx-users] File editing - only one layer of water around a molecule

Re: [gmx-users] File editing - only one layer of water around a molecule On 12/04/2012 3:24 AM, Justin A. Lemkul wrote: > > > Lara Bunte wrote: >> Could you please give how g_select is used? Reading g_select -h might have led you to try g_select -select 'help' >&

Re: [gmx-users] File editing - only one layer of water around a molecule

a molecule Please leave the discussion on the mailing list, so that others can contribute and benefit now and via the archives. On 11/04/2012 10:53 PM, Lara Bunte wrote: Hi > > >How to do that? I searched the manual for "layer" and I don't find something >that

Re: [gmx-users] File editing - only one layer of water around a molecule

Lara - Ursprüngliche Message - Von: Mark Abraham An: Discussion list for GROMACS users CC: Gesendet: 14:27 Mittwoch, 4.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/04/2012 7:27 PM, Lara Bunte wrote: > Hello > > I h

[gmx-users] File editing - only one layer of water around a molecule

Hello I have a question about editing a pdb file. I have a molecule in a box of water as a pdb file. I want to remove all water except of ONE layer around he molecule.  How to do that? Do you know a software that is able to do that? Do you know how it could work with programs like PyMol or o

[gmx-users] Shape of box

Hello If you add solvent water around your protein you have to generate a box with the editconf command. How to know what shape that box should have? In my tutorial is a dodecahedron used. What other boxes exist and how to know which box one has to use? Thanks Greetings Lara -- gmx-users mail

[gmx-users] System exploding

Hello If gromacs gives the warning that the system could explode, what could be the reason for that? Greetings -- 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

Re: [gmx-users] Equilibrate the water around my molecule

has to do with this termini? Thanks Greetings Lara - Ursprüngliche Message - Von: Mark Abraham An: Discussion list for GROMACS users CC: Gesendet: 15:28 Montag, 26.März 2012 Betreff: Re: [gmx-users] Equilibrate the water around my molecule On 26/03/2012 11:55 PM, Lara Bunte wro

Re: [gmx-users] Equilibrate the water around my molecule

he Message - Von: Mark Abraham An: Discussion list for GROMACS users CC: Gesendet: 14:45 Montag, 26.März 2012 Betreff: Re: [gmx-users] Equilibrate the water around my molecule On 26/03/2012 11:21 PM, Lara Bunte wrote: > Hi > > I changed in my residuetypes.dat file ISO Isoalloxazi

Re: [gmx-users] Equilibrate the water around my molecule

AM, Lara Bunte wrote: > Hello > > I want to equilibrate the water around my (small) molecule. In the tutorials > I found and in the manual is not enough information how to do that if you > have an own parametrization of a molecule. > > > Here is my situation: > >

[gmx-users] Equilibrate the water around my molecule

Hello I want to equilibrate the water around my (small) molecule. In the tutorials I found and in the manual is not enough information how to do that if you have an own parametrization of a molecule. Here is my situation: I have a pdb file and I have a parametrization for this molecule out o

[gmx-users] Box Size in MD

Hello What size should a box have in that you do your MD? I always read that for short Lennard Jones interactions one should do a cut off with the half of the box size but what how to know a good box size? Thanks for help Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://

[gmx-users] Group protein not found in index file

Hello I want to use the command  grompp -n index.ndx -f pr.mdp -p topol.top -c em.gro -o pr.tpr and I got the error: Fatal error: Group protein not found in index file. Group names must match either [moleculetype] names or custom index group names,in which case you must supply an index file

Re: [gmx-users] grompp - Group protein not found

your knowledge about what is a protein, * name your [moleculetype] the same as your references to it in your .mdp file and [molecules] section. Mark > > > On 2012-03-07 05:13:11PM +, Lara Bunte wrote: >> Hi >> >> I create a file pr.mdp for equilibratin

[gmx-users] nrexcl in topology

Hi in a topology file in the section [ moleculetypes ] is standing ; nrexcl     3 What do this mean? Thanks for help Greetings Lara -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Suppo

[gmx-users] Information on .mdp files

Hello I want to learn how to create a .mdp file and learn what I can write in such a file and learn what the entries in this file are meaning. I did not find this in the manual. Could you please give me link or some source where I can find this information? Thanks and best greetings Lara -- g

Re: [gmx-users] grompp - Group protein not found

t;protein," * copy $GMXLIB/residuetypes.dat to your working directory and add your protein residues to allow the default generated groups to understand your knowledge about what is a protein, * name your [moleculetype] the same as your references to it in your .mdp file and [molecules] secti

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

s do not. -Justin > On 2012-03-07 05:19:19PM +, Lara Bunte wrote: >> Hi Justin >> >> >> I am using a CHARMM27 force field. I create a pdb file with the coordinates >> of my molecule and I create a .rtp and a .hdb file for this. I also edit >> atomtyp

Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology

, 6.März 2012 Betreff: Re: [gmx-users] Missing Interactions in [ angles ] Section in Topology Lara Bunte wrote: > Hi > > In some lines the equilibrium angle and the force constant is missing.I give > you an example: > > > The [ angles ] section is build like > > [ a

[gmx-users] grompp - Group protein not found

Hi I create a file pr.mdp for equilibrating the water around my molecule and used after that the command grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr And I got tthe error: Fatal error: Group protein not found in index file. Group names must match either [moleculetype] names or custom inde

[gmx-users] mdrun - topol.tpr

Hi After I used grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr to collect my files into one em.tpr file (which is the meaning of gromp as fas as I understand it) Then I start mdrun for energy minimization with the command mdrun -nt 1 deffnm em and got the error Can not open file:

[gmx-users] Missing Interactions in [ angles ] Section in Topology

Hi After pdb2gmx are in the [ angles ] section some lines missing and I am pretty sure that they are defined in my .rtp file in my force field folder. There are also just a few lines mission, most of the angles are in topology. I know the parameters so I can add it by hand to topology but what

[gmx-users] Two [ dihedrals ] Sections in Topology

Hi After pdb2gmx I got two [ dihedrals ] sections in the topology file. [ dihedrals ]   ai    aj    ak    al funct    c0    c1    c2    c3    c4    c5     2 1    19 8 5     6 8 9    10 5     6 8    19 1 5 [ di

[gmx-users] [ pairs ] section in topology

Hi My topology file which I get after pdb2gmx has in one section following section: [ pairs ] ;  ai    aj funct    c0    c1    c2    c3     1 5 1     1 6 1     1 9 1     1    17 1 Is it correct that there are no entries in c0, c1, c2 a

[gmx-users] grompp - Invalid command line argument

Hi I used the command grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr and got the error Source code file: /home/adrian/src/gromacs-4.5.5/src/gmxlib/statutil.c, line: 819 Invalid command line argument: em.tpr What is the problem here? Greetings Lara -- gmx-users mailing listgm

[gmx-users] grompp error - bondedtypes

Hi I used the command grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr and get this errors: ERROR 1 [file flavin.rtp, line 1]:   Invalid directive bondedtypes ERROR 2 [file flavin.rtp, line 7]:   Not enough parameters I know where this error occurs from but I don't know what is fa

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