Re: [gmx-users] dssp and gromacs version

On 2/03/2012 6:52 PM, lina wrote: Hi, is the old dssp not compatible with the gromacs 4.5.5 ? I am confused, Thanks, Best regards, The new DSSP is not compatible with any GROMACS Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Ple

[gmx-users] dssp and gromacs version

Hi, is the old dssp not compatible with the gromacs 4.5.5 ? I am confused, Thanks, Best regards, -- 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 posti

Re: [gmx-users] MDrun append...

On 2/03/2012 3:59 PM, rama david wrote: Dear GROMACS Friends, my MD run get crashed , I foollow following command .. mdrun -s protein_md.tpr -c protein_md.trr -e protein_md.edr -g protein_md.log -cpi -append -v the system respond in a way.. Fatal error: The original run wrote a file called

[gmx-users] MDrun append...

Dear GROMACS Friends, my MD run get crashed , I foollow following command .. mdrun -s protein_md.tpr -c protein_md.trr -e protein_md.edr -g protein_md.log -cpi -append -v the system respond in a way.. Fatal error: The original run wrote a file called 'traj.trr' which is larger than 2 GB, but m

RE: [gmx-users] dihedral distributions

1 - Those two index groups refer to two different dihedrals within your topology, and the labeling of them will come from something about the dihedral, more than likely it is from the force constant. 2 - if it starts asymmetric, then with time becomes symmetric, that may be an indicator of reac

Re: [gmx-users] dihedral distributions

Hi all, I used the following line to obtain index file of RB dihedral quadrupltes: mk_angndx -s *.tpr -n *-RB -type ryckaert-bellemans The resulting index file contains two groups [ RB-A1=1.88 ] [ RB-A1=-1.46 ] 1- Can anyone tell me please what these groups refer to? I am not able to find the

Re: [gmx-users] mdrun -multi flag

On 2/03/2012 10:15 AM, bo.shuang wrote: Hello, all, I am trying to do REMD simulation. So I used command: mdrun -s t2T.tpr -multi 2 -replex 1000 And gromacs gives error report: Fatal error: mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support For more

[gmx-users] mdrun -multi flag

Hello, all, I am trying to do REMD simulation. So I used command: mdrun -s t2T.tpr -multi 2 -replex 1000 And gromacs gives error report: Fatal error: mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support For more information and tips for troubleshooting, p

Re: [gmx-users] Segmentation fault - Implicit solvent

On Thu, Mar 1, 2012 at 10:26 PM, Mark Abraham wrote: > On 2/03/2012 9:22 AM, Steven Neumann wrote: > > > > On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul wrote: > >> >> >> Steven Neumann wrote: >> >>> >>> >>> On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote: >>> >>>

Re: [gmx-users] Segmentation fault - Implicit solvent

On 2/03/2012 9:22 AM, Steven Neumann wrote: On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul mailto:jalem...@vt.edu>

Re: [gmx-users] Segmentation fault - Implicit solvent

On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> >> >> On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Steven Neumann wrote: >> >> >> >>On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann >>mailto:s.neu

Re: [gmx-users] Random option - genion

On 2/03/2012 4:42 AM, Justin A. Lemkul wrote: Maurício Menegatti Rigo wrote: Dear users, can anyone tell me if the random option (genion program) was set to always stay in the "yes" state? I'm trying to set "-random no" (just a test), but it didn't work at all. The default is "yes." To i

Re: [gmx-users] Segmentation fault - Implicit solvent

Steven Neumann wrote: On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann mailto:s.neuman...@gmail.com>

Re: [gmx-users] Segmentation fault - Implicit solvent

On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> >> >> On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann > s.neuman...@gmail.com>**> wrote: >> >> >> >>On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann >>mailto:s.neuman...@gmail.com>**> wrote: >> >> >> >>

Re: [gmx-users] genconf -renumber merges atom number and ID columns

I thank you for the answer Justin. Indeed, the fixed format of the .gro file is respected, therefore this is a non-problematic issue. I'm having no problems with this spacing, It was just something I was wondering about. Well, anyway, thanks again. Ricardo. >

[gmx-users] Test particle insertion extra coordinate

Hi everyone. I am trying to do test particle insertion in a cavity with the tpic option. The manual says that the trajectory file should have one extra coordinate for the cavity location. I have a trajectory from an md run that I would like to use. How do I get the extra coordinate in there, and wh

Re: [gmx-users] genconf -renumber merges atom number and ID columns

Ricardo O. S. Soares wrote: Dear gmx users, After merging two .gro files, I set a new numbering with genconf -renumber. My results show that from the 1th atom, the atom number and its ID are no longer separated by at least one space: 75POP C216 9998 0.705 4.657 3.200 0.000

Re: [gmx-users] Random option - genion

Thank you very much, Justin. Mauricio 2012/3/1 Justin A. Lemkul > > > Maurício Menegatti Rigo wrote: > >> Dear users, >> >> can anyone tell me if the random option (genion program) was set to >> always stay in the "yes" state? I'm trying to set "-random no" (just a >> test), but it didn't work a

[gmx-users] genconf -renumber merges atom number and ID columns

Dear gmx users, After merging two .gro files,  I set a new numbering with genconf -renumber. My results show that from the 1th atom, the atom number and its ID are no longer separated by at least one space:    75POP   C216 9998   0.705   4.657   3.200  0.  0.  0.    75POP   H16

Re: [gmx-users] Segmentation fault - Implicit solvent

Steven Neumann wrote: On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann > wrote: On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann mailto:s.neuman...@gmail.com>> wrote: On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul mailto:jalem...@vt.e

Re: [gmx-users] Random option - genion

Maurício Menegatti Rigo wrote: Dear users, can anyone tell me if the random option (genion program) was set to always stay in the "yes" state? I'm trying to set "-random no" (just a test), but it didn't work at all. The default is "yes." To invoke the opposite (which is true for all Gro

[gmx-users] Random option - genion

Dear users, can anyone tell me if the random option (genion program) was set to always stay in the "yes" state? I'm trying to set "-random no" (just a test), but it didn't work at all. Thanks in advance, Mauricio -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

Re: [gmx-users] Segmentation fault - Implicit solvent

On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann wrote: > > > On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann wrote: > >> >> >> On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul wrote: >> >>> >>> >>> Steven Neumann wrote: >>> Dear Gmx Users, I am trying to run nvt simulation (equilibratio

Re: [gmx-users] Segmentation fault - Implicit solvent

On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann wrote: > > > On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul wrote: > >> >> >> Steven Neumann wrote: >> >>> Dear Gmx Users, >>> I am trying to run nvt simulation (equilibration) of the protein in >>> implicit solvent. My mdp: >>> >>> integrator =

Re: [gmx-users] Segmentation fault - Implicit solvent

On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Dear Gmx Users, >> I am trying to run nvt simulation (equilibration) of the protein in >> implicit solvent. My mdp: >> >> integrator = md ; leap-frog integrator >> >> nsteps = 100 ; 0.0005 * 100 = 0.

Re: [gmx-users] Segmentation fault - Implicit solvent

Steven Neumann wrote: Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp: integrator = md ; leap-frog integrator nsteps = 100 ; 0.0005 * 100 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 1 nstxtcout = 1

[gmx-users] Segmentation fault - Implicit solvent

Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp: integrator = md ; leap-frog integrator nsteps = 100 ; 0.0005 * 100 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 1 nstxtcout = 1 ; xtc compressed trajecto

[gmx-users] Re: Umbrella Sampling - ligand

Steven Neumann wrote: Dear Gmx Users, Dear Justin, I run Umbrella Sampling for my ligand pulling using Justin's Tutorial. Please, see attached my histogram and PMF profile. I know it requires more sampling around distance from 0.8 to 2.5 nm. 1) Will more sampling affect the final deltaG wh

[gmx-users] reverse transformation with dihedral restraints

Hello, I'm trying to do a reverse transformation from coarse grained to all atom following the MARTINI tutorial and applying it to my system. I have manually added the dihedral restraint section to my topology and now, when I try to run the g_fg2cg command I get the following error: calling cpp...

[gmx-users] new OPLS-AA dihedral parameters for hydrocarbons ?

Dear All I was checking the OPLS-AA dihedral terms for modeling an alcohol-like molecule. I plotted the torsional energy for the dihedrals formed by these atomtypes: CT CT CT HC, CT CT CT CT, HC CT CT HC, CT CT CT OH, OH CT CT HC using the parameters in the OPLS-AA ffbonded.itp file of GROMACS

Re: [gmx-users] PBC - Protein and Ligands

Thank you all! That helped a lot! Steven On Wed, Feb 29, 2012 at 5:17 PM, Vedat Durmaz wrote: > ** > i always did it (successfully) with one single command: > > trjconv -f md.trr -s md.tpr -o mdCompact.trr -pbc mol -ur compact -n > ../../index.ndx > > > regards > vedat > > > Am 29.02.2012 18:01

Re: [gmx-users] using g_angle

Hi all! I have a question about how g_angle works. Form what I understood from the manual, if I provide an index file with dihedral quadruplets, then g_angle with the options -ov -all and -type dihedral should give me a list of dihedral values one for each quadruplet. However when I do that I obtai