[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

[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

[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

[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

[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

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 p...@uab.edu An: Lara Bunte lara.bu...@yahoo.de CC: gmx-users@gromacs.org gmx-users

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

mdrun -nt number # of mdrun 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

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 p...@uab.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 17:58 Montag

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

totaly frustrated and shortly for giving it up :-(:-( :-( Best greetings Lara - Ursprüngliche Message - Von: Peter C. Lai p...@uab.edu An: Lara Bunte lara.bu...@yahoo.de CC: gmx-users@gromacs.org gmx-users@gromacs.org Gesendet: 17:57 Montag, 24.September 2012 Betreff: Re: [gmx-users

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

. Lai p...@uab.edu An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Lara Bunte lara.bu...@yahoo.de 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

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

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)  =  1.0e+03     Number of steps    =        5000 Stepsize

[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

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

- Ursprüngliche Message - Von: Justin Lemkul jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 16:04 Freitag, 21.September 2012 Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error On 9/21/12

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

Lara - Ursprüngliche Message - Von: Justin Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org 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

[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] 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.

[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

Re: [gmx-users] Energy Minimization of Alanin

). On 2012-09-19 11:04:47AM +0100, 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

[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

[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] 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

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 jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 16:04 Dienstag

[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

Re: [gmx-users] Structure optimization failure

the 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 jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 12:23

[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

[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

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 mrshi...@gmail.com An: Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 18:24 Freitag, 1.Juni 2012 Betreff:

[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

[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

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

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 jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list

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 richard.broadben...@imperial.ac.uk An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: jalem...@vt.edu jalem...@vt.edu

[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

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

, 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. An empty block

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

jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org 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

[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] Force Constants and Unit Systems

this values. Could you please explain this? Greetings and really thanks for your help Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 18:52 Donnerstag, 17.Mai

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

Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 19:18 Donnerstag, 17.Mai 2012 Betreff: Re: [gmx-users] Force Constants and Unit Systems Hi Lara, On Thu, 2012-05-17 at 17:58 +0100, Lara Bunte wrote: Hi One cannot convert between

[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

[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:

Re: [gmx-users] grompp Unkown bond_atomtype C2

...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org 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

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

- Ursprüngliche Message - Von: Mark Abraham mark.abra...@anu.edu.au An: Discussion list for GROMACS users gmx-users@gromacs.org 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 Bunte wrote: Hi After

[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] 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

Message - Von: Justin A. Lemkul jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org 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

[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

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 jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 20:32 Montag, 14

[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

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

] 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 filled in with existing parameters from [angletypes] in ffbonded.itp. I let the lines empty and I got an error at the first grompp, before energy

[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

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

- Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org 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

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

- Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org 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

[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

[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

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

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

- Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org 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, Lara Bunte wrote

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

Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org 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

[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

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

for helping me. Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 18:07 Montag, 30.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around

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

Message - Von: Justin A. Lemkul jalem...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org 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: Hi Justin I got

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

...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org 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

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

...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org 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

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

@gromacs.org CC: Gesendet: 18:39 Montag, 23.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 trjconv -s -f

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

An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 19:20 Montag, 23.April 2012 Betreff: Re: [gmx-users] File editing - only one layer of water around a molecule On 4/23/12 1:13 PM, Lara Bunte wrote: Hi If I use trjconv -n index.ndx -f

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

...@vt.edu An: Discussion list for GROMACS users gmx-users@gromacs.org 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 -s molecule_in_water.pdb -select 'Close

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

, Lara Bunte wrote: Hi Justin You wrote:   If you do not specify any output file, the default is this .xvg file that tells you how many atoms satisfied the criterion specified in the selection string. If you want a coordinate file, it's a two-step process.     1. Run g_select using

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

: Teemu Murtola teemu.murt...@cbr.su.se An: Discussion list for GROMACS users gmx-users@gromacs.org 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 lara.bu...@yahoo.de wrote

[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

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

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? Von: Justin A. Lemkul jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org Gesendet

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 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

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 (valences closed by hydrogen

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 jalem...@vt.edu An: Lara Bunte

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

@gromacs.org Gesendet: 12:06 Freitag, 13.April 2012 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

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 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 for -f and -s. Like

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

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 jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org Gesendet: 14:59 Freitag

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

, 13.April 2012 Betreff: Re: [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: selection parser: invalid selection 'Close

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

- Ursprüngliche Message - Von: Mark Abraham mark.abra...@anu.edu.au An: Discussion list for GROMACS users gmx-users@gromacs.org 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

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

] File editing - only one layer of water around 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

[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

[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

[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

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

the water around my molecule On 24/03/2012 5:38 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

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

- Von: Mark Abraham mark.abra...@anu.edu.au An: Discussion list for GROMACS users gmx-users@gromacs.org 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

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

/2012 11:55 PM, Lara Bunte wrote: Hi my command was pdb2gmx -f isoalloxazin.pdb -water tip3p which worked for ISO Isoalloxazin in the residuetypes.dat Sure, because pdb2gmx had not been told that ISO was protein, it didn't try to treat it as protein. I don't get an output of this command

[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

[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

[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

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

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 equilibrating the water around my molecule and used after

[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] Missing Interactions in [ angles ] Section in Topology

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 atomtypes.atp, ffnonbonded.itp and residuetypes.dat The parameters

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

+, Lara Bunte wrote: 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

[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

[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

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

@gromacs.org 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 equilibrium angle and the force constant is missing.I give you an example: The [ angles ] section is build like

[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 list

[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

[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 [

[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] [ bondedtypes ]

Thanks for your help. :-)  I did not realize that table 5.5 corresponds to [ bondedtypes ] 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_Lists/Search

[gmx-users] How to answer in this mailing list?

Hello I wrote an email to the mailing list with the subject [ bondedtypes ] and I got answers that helped me. I wanted to answer to this by a new email with same subject and the mailing list create a new question out of it. How do I answer in this mailing list to a topic? Thanks Greetings

Re: [gmx-users] How to answer in this mailing list?

Hi Thanks for answer. This is also a test if it work :-) 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_Lists/Search before posting! Please don't post

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