Re: [gmx-users] Re: Structure preparation for the simulation

://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- "In theory, there

Re: [gmx-users] Gromacs versions 4.0.5 and 4.5.4

ber. > constraint_algorithm = shake Any reason why not to using LINCS? - "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral

Re: [gmx-users] Gromacs versions 4.0.5 and 4.5.4

:14 PM, Sapna Sarupria wrote: > Dear Itamar, > > Thank you for your response. Why did you prefer to stick to 4.0.7? Is there > something particularly difficult to transfer from 4.0.7 version to 4.5 > version? > > Sapna > > On Tue, Oct 18, 2011 at 9:36 PM, Itamar Kass

Re: [gmx-users] Gromacs versions 4.0.5 and 4.5.4

are of that. Still, the fact that the SD integrator also solves the problem also suggests that this is simply a poorly equilibrated system. I am not sure why PME would run fine and reaction field would give lincs warnings, but then again I have no experience with using a reaction field. Chris. On 1/

Re: [gmx-users] "Simulation" of a crystal

between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

after equilibrating using > productions conditions. It it solves it, maybe the option should be > renamed nstptrouble :p > > Hope it helps, > > Tsjerk > > On Thu, Sep 1, 2011 at 7:43 AM, Itamar Kass wrote: >> HI Chris, >> >> I am sorry that from my mails it is

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

he case of 981 and 982, and sometimes others. In > addition, there is no visible difference in dynamics between 4.0.7 and 4.5.4 > I can find. > > Itamar > > > On 01/09/2011, at 11:14 AM, Justin A. Lemkul wrote: > >> >> >> Itamar Kass wrote: >>

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

times others. In addition, there is no visible difference in dynamics between 4.0.7 and 4.5.4 I can find. Itamar On 01/09/2011, at 11:14 AM, Justin A. Lemkul wrote: > > > Itamar Kass wrote: >> Hi Mark, >> I didn't had the time to do the SD yet, but serial run e

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

ough. >>>> >>>> Chris. >>>> >>>> Hi Chris and Justin, >>>> >>>> On 18/08/2011, at 9:36 AM, Justin A. Lemkul wrote: >>>> >>> >>> -- >>> gmx-users mailing listgmx-users@gromacs

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

ling_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists - "In theory, there is no difference between t

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time

l considerations (distance restraints, >> modified parameters, etc). An .mdp file would also be useful for the run >> that crashes. > > The only constraints I had in the system LINCS of all bonds. I didn't > modified the FF in anyway. > > Best, > Itamar &

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

rch before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists - "In theory, there is no difference between theory and practice.

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

Dear Mark, We also tried to minimise the system in vacuum before adding water and ions withou, but it still crashed when we did MD. Itamar. On 18/08/2011, at 10:31 AM, Mark Abraham wrote: > On 18/08/2011 10:14 AM, Itamar Kass wrote: >> >> Hi Chris and Justin, >> >

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

Zwier wrote: >>> Could be a system blowing up, or perhaps a mis-compiled binary. What >>> error messages do you get when the crash occurs? >>> >>> On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass >>> wrote: >>> > Hi all GROMACS useres and devel

Re: [gmx-users] GROMACS 4.5.4 keep crashing all the time.

mpiled binary. What > error messages do you get when the crash occurs? > > On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass > wrote: > > Hi all GROMACS useres and developers, > > > > I am interesting in simulating a small protein (~140 aa) in water, with > and without

[gmx-users] GROMACS 4.5.4 keep crashing all the time.

;In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut ======= | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Camp

Re: [gmx-users] Simulation a labeled protein

Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@

[gmx-users] malloc on mac

Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail

Re: [gmx-users] maintained an Hbond using a distance restraint

Thanks! Itamar. On 14/07/11 11:53 AM, Justin A. Lemkul wrote: Itamar Kass wrote: Hi Justin, Thanks for the quick replay. Regrading Q.1 that was my idea, just wanted to be sure. Regarding Q.2, I think a more relevant phrase would be, how big a force I can use without cancel the "val

Re: [gmx-users] maintained an Hbond using a distance restraint

use 2 for type', is this mean there is no time averaging? If so, is there any meaning for disre_tau> Cheers, Itamar On 14/07/11 11:41 AM, Justin A. Lemkul wrote: Itamar Kass wrote: Hi, I wish to force my system to maintained an Hbond during a simulation. In order to do so I a

[gmx-users] maintained an Hbond using a distance restraint

e. But, in practice, there is." - Jan L.A. van de Snepscheut ======= | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3

Re: [gmx-users] problem during energy minimization before MD

t; > > [ molecules ] > > ; Compound#mols > > Protein_A 1 > > DPPC121 > > > > SOL 11107 > > CL- 14 > > > -----

Re: [gmx-users] dealing with ATP

users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read ht

Re: [gmx-users] any software which could convert a polypeptide sequence to a pdb file?

n de Snepscheut ======= | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 990

Re: [gmx-users] No cut-off

ctice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | |

Re: [gmx-users] Protein-membrane system

theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Ca

Re: [gmx-users] General MD question

end it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut =

Re: [gmx-users] transmembrane protein simulation

alakshmi N -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut ======= | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology |

[gmx-users] problem when calculating the solvation free energy of ARG in water using PME.

re is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3

Re: [gmx-users] md.log

Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 950

Re: [gmx-users] dna, lipid simulation

en theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victor

Re: [gmx-users] Simulation parameter problem about protein unfolding

tice, there is." - Jan L.A. van de Snepscheut ======= | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia |

[gmx-users] Problems when simulating a protein in its crystal matrix.

here is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut ======= | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellingto

Re: [gmx-users] Query regarding protonation and deprotonation of some residues

dynamics simulation in Gromacs. Thanks and Regards. -- Sonali Dhindwal -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctora

Re: [gmx-users] g_cluster cutoff

ry, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | W

Re: [gmx-users] Protein stability using MARTINI

Thanks Mark for the replay, I used VDW presentation to over come it. Best, Itamar On 6/09/2010 6:33 PM, Mark Abraham wrote: - Original Message - From: Itamar Kass Date: Monday, September 6, 2010 14:06 Subject: [gmx-users] Protein stability using MARTINI To: Discussion list for

Re: [gmx-users] the broken of the molecules

you very much ! // -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecul

[gmx-users] Protein stability using MARTINI

coil tail, as I wish to capture as much conformation as possible. Thanks in advance, Itamar. -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut ======= | Itamar Kass, Ph.D.

[gmx-users] TI calculation in vacuum gives number which is not zero for small molecule.

dl for the last 1ns (out of 1.1ns). Any idea why this happen? All the best, Itamar -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut ======= | Itamar Kass, Ph.D. | Pos

Re: [gmx-users] CG (MARTINI) parameters for RNA

else from the Khalid group) will let the list know when and where they have been made available. Cheers Tom Itamar Kass wrote: Shalom all, I wish to try and simulate a protein with few RNA bases attached. As I favour speed over accuracy in this case I wish to use the MARTINI model. I could

[gmx-users] CG (MARTINI) parameters for RNA

force field? All the best, Itamar -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Bioche

Re: [gmx-users] rmsd between different monomers

y and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Vic

Re: [gmx-users] Simulation of only Lipid Bilayer

he procedure using Gromacs? Hoping for some inputs. Regards Saumya -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Resear

[gmx-users] Subtraction of xpm files

, Itamar -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | B

Re: [gmx-users] temperature

. Best, Itamar -- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecul

Re: [gmx-users] indexing and new molecules

Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 950

[gmx-users] indexing and new molecules

theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut ======= | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University,

[gmx-users] g_cluster group for output

tween theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Mona

Re: [gmx-users] grompp in GROMACS 4

Hi, you don't use -np ??? anymore, GROMACS use all the available (MPI connected )CPU. On 4/02/10 2:55 PM, Mark Abraham wrote: On 04/02/10 14:42, edmund lee wrote: Dear all, I am new in Gromacs 4.0.7 before this I was using the GROMACS 3.3.3. I have some doubt in the grompp commands when

Re: [gmx-users] atomnumber=-12345

dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Itamar Kass *Sent:* Thursday, 21 January 2010 11

[gmx-users] atomnumber=-12345

ctice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Vic

Re: [gmx-users] 6LYZ.pdb + Gromacs version 4.0.5 => Simulation Broken (output file)

Hi, It is not clear to me if you did EM or not. If you didn't, it is highly advisable to do short EM before you start your PR step. Best, Itamar On Sun, Jan 10, 2010 at 1:29 PM, Chih-Ying Lin wrote: > > Hi > 6LYZ.pdb is simply a lysozyme structure and I merely solvated it running > the simulati

Re: [gmx-users] RMSD Vs Residue no by Grace

Hi, RMSD is given at a specific time, so you can ran g_rms for each residue (create index file witha specific residue in) and then take the RMSD of each residue at time T and plot it. But I think you should look into g_rmsf, this might fit you better, although it calculate the fluctuations rather

Re: [gmx-users] (no subject)

On 27/11/09 3:15 AM, pawan raghav wrote: I have used GROMACS 4.0.5 on windows can anyone tell me about how to get em.mdp, and pr.mdp file for my protein. -- Pawan Hi, A good place to start and learn about mdp files is http://www.gromacs.org/Documentation/Tutorials. You can find lot of tuto

Re: [gmx-users] pdb2gmx -missing

s may confuse the original > poster and bring them even further from solving their problems. > > Cheers, > > Tsjerk > > On Wed, Nov 11, 2009 at 9:16 AM, Itamar Kass wrote: >> Hi, >> >> Try to use -ignh. >> >> On Wed, Nov 11, 2009 at 7:

Re: [gmx-users] pdb2gmx -missing

Hi, Try to use -ignh. On Wed, Nov 11, 2009 at 7:09 PM, leila karami wrote: > I do command pdb2gmx but follow warning and error is came up: > > WARNING: atom H is missing in residue GLY 1 in the pdb file > You might need to add atom H to the hydrogen database of residue > GLY >

[gmx-users] solvation energy calculation

ot;In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clay

Re: [gmx-users] MD with bilayer

Hi, VMD was built to work with NAMD, so the atom names and topologies will not work with GROMACS. I guess you better go to Peter Tieleman site ( http://moose.bio.ucalgary.ca/) and rad there how to do things. Cheers, Itamar On Tue, Nov 10, 2009 at 8:05 AM, Mark Abraham wrote: > parthi...@ncbs.re

Re: [gmx-users] Re : Gromacs 4.0 parallelization

Hi, I think it is more important how you compiled you gromacs. Had you used --enable-mpi? Itamar On Sun, Nov 8, 2009 at 2:08 AM, milad ekramnia wrote: > Hi Mark > my mdrun command line is : > mpirun -n 4 mdrun_mpi -v -s topol.tpr > > regards > -- > Milad Ekramnia > Physics Department > Isfahan

Re: [gmx-users] minimization problem

anyway about emstep? Payman On Mon, 2009-10-26 at 10:43 +1100, Itamar Kass wrote: I am not sure what you refer to as dt, as there no meaning to time in EM. Anyway, I think the easiest way is to remove this ware molecule. Best, Itamar. On 26/10/2009, at 10:31 AM, Paymon Pirzadeh wrote: Hello, I

Re: [gmx-users] minimization problem

I am not sure what you refer to as dt, as there no meaning to time in EM. Anyway, I think the easiest way is to remove this ware molecule. Best, Itamar. On 26/10/2009, at 10:31 AM, Paymon Pirzadeh wrote: Hello, I merged two simulation boxes, and now I want to perform a minimization to re

Re: [gmx-users] simulation end with Segmentation fault, error message said something about libSystem.B.dylib

On Thu, Oct 15, 2009 at 1:40 PM, Mark Abraham wrote: > Itamar Kass wrote: > >> Hi, >> >> Lately few of my simulations had ended up with wired output: >> >> Writing final coordinates. >> step 50, remaining runtime: 0 s [xn068:94365] **

[gmx-users] simulation end with Segmentation fault, error message said something about libSystem.B.dylib

Hi, Lately few of my simulations had ended up with wired output: Writing final coordinates. step 50, remaining runtime: 0 s [xn068:94365] *** Process received signal *** [xn068:94365] Signal: Segmentation fault (11) [xn068:94365] Signal code: Address not mapped (1) [xn068:94365] Failing a

Re: [gmx-users] run g_cover in parallel

ot;. So I guess there are more parallel things then just MD. Cheers, Itamar On Wed, Oct 14, 2009 at 10:48 AM, Mark Abraham wrote: > Itamar Kass wrote: >> >> Hi, >> >> I wonder if there a way to run g_cover in paralel in order to make >> things run faster? > >

[gmx-users] run g_cover in parallel

Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail

Re: [gmx-users] Problem in equilibration for membrane system

between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut ======= | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash Un

Re: [gmx-users] water molecule cannot be settled

a beginner with gromacs and all I found about gmxdump is that it reads a binary file & prints that to standard output in a readable format. So how can I check if my atom number is the same in my pdb file & my output file? Carla On Wed, Sep 30, 2009 at 4:38 AM, Itamar Kass <mailto:ita

Re: [gmx-users] water molecule cannot be settled

ctice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Vic

Re: [gmx-users] System has non-zero total charge: 2.570000e+00

Justin A. Lemkul wrote: najwa drici wrote: hello Gromacs users, I have some problems about the total charge of system using Gromacs. I wanted to perform molecular dynamic simulation in box of SPC water. before energy minimization step , I performed the preprosessing step using grompp . How

[gmx-users] grompp results in Segmentation fault

Hi, I have installed GROMACS 4.0.5 on our cluster (gcc 4.2.1, Open MPI 1.2.3) whereas only mdrun was install with -enable-mpi flag. When I try to run it via a script (grompp -f pr_complex.mdp -c complex_from_EM.gro -p complex.top -n complex.ndx -po complex_from_PR.mdp -o complex_for_PR.tpr) I get

[gmx-users] grompp crashes when submitted to the cluster

Segmentation fault grompp Any idea? Cheers, Itamar --- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Resea

[gmx-users] grompp crashes when submitted to the cluster

Segmentation fault grompp Any idea? Cheers, Itamar --- "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Dep

[gmx-users] Using Myrinet, openmpi 1.3.3 and GROMACS 3.3.2

tice, there is." - Jan L.A. van de Snepscheut === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77 Clayton Campus | Wellington Road | Monash University, | Victoria 3800 | Australia | | Tel: +61 3 9

Re: [gmx-users] waters in ion channels

Hi, I would say that those are water molecule which enter from the bulk water. This is normal and probably important for the physiological function of the system. Best, Itamar On Fri, Jul 3, 2009 at 8:08 PM, Samik Bhattacharya wrote: > hi i'm simulating a ion channel protein in DPPC membrane. i'

Re: [gmx-users] segfault(11) -- simulation blows up on first step

Hi, I don't see any immediate problem in your file, except the fact that you have to couple all molecule to a heat bath. Second, has much as I know, you can't reach 0K, so what the meaning? Best, Itamar On Tue, Jun 2, 2009 at 9:11 PM, Inon Sharony wrote: > Hi everyone! > > I'm trying to run a

[gmx-users] mpi problem during installation

HI all, I am trying to compile GROMACS 4.0.5 on my mac (10.5) using './configure --enable-mpi --disable-float --with-fft=no && make -j2 && make install'. I installed on the system lam 7.0.6 './configure && make && make install'. The error message I get is: mpicc -O3 -fomit-frame-pointer -finline

[gmx-users] Biomolecular Modelling Retreat 8-12th September 2008

end in time for the students to attend the young scientists forum of WATOC in Sydney. More details can be found at: http://compbio.chemistry.uq.edu.au/MDschool/Main.html -- === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Molecular Dynamics

Re: [gmx-users] Extending MD run

e use in your case. Choose a frame that is present in both your .edr and .trr, and specify this time as your restart point with the -time option. -Justin Quoting Itamar Kass <[EMAIL PROTECTED]>: Hi all, In gromacs if you want to extend your run you can do something like > grompp_d -f

[gmx-users] Extending MD run

Hi all, In gromacs if you want to extend your run you can do something like > grompp_d -f md.mdp -c MD1.gro -p mol.top -t rom_MD1.trr -e from_MD1.edr -o for_MD2.tpr Now my question is, what happen if the trr file ends at 400ps and the edr file ends at 399ps? Will it use the trr alone and for

RE: [gmx-users] errores during compilation of GROMACS 3.3.2

as changed in the intel compiler or assembler lately... Cheers, Erik On Oct 15, 2007, at 10:34 AM, Itamar Kass wrote: > > Dear Erik, > > I had compiled the 3.3.1 on the same machine. The sys admin of this > machine is been able to compile 3.3.2 using the gnu compiler but >

RE: [gmx-users] errores during compilation of GROMACS 3.3.2

16 AM, Itamar Kass wrote: > Dear all, > > I am trying to compile GROMOCS 3.3.2 on Altix 3700 BX2 (Itanium2 > 1.6GHz). I am doing something like: > > > ./configure --prefix=/home/564/ixk564/software/gromacs --enable- > shared --program-suffix=_3.3.2_double --disable-float

[gmx-users] errores during compilation of GROMACS 3.3.2

Do you have any idea how to overcome it? Best wishes, Itamar. -- "Prediction is very difficult, especially about the future" - Niels Bohr === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Molecular Dynamics Group | School of Molecular a

Re: [gmx-users] simulation popc

.org/mailing_lists/users.php -- "Prediction is very difficult, especially about the future" - Niels Bohr === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Molecular Dynamics Group | School of Molecular and Microbial Sciences (SMMS) | Chemistry Building (#68) | The Univers

RE: [gmx-users] protein in membrane

Shalom, The easy way is to remove lipids such that a hole in the membrane will form, put your protein in in run. Or you can try the protocol in Faraldo-Gomez, J. D., Smith, G. R., and Sansom, M. S. (2002) "Setting up and optimization of membrane protein simulations. European Biophysics Journa

Re: [gmx-users] puting things in

Hi Mark, I thought I was clear. I want to have a gro file in which all the peptide are in the same side of the membrane and with the minimum distance between them (lowest distance between mirror images). Thanks again, Itamar. Mark Abraham wrote: Itamar Kass wrote: I wish to cut the box now

[gmx-users] puting things in

list and more without any success. Thanks all, Itamar -- "Prediction is very difficult, especially about the future" - Niels Bohr ======= | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | | Molecular Dynamics Group | School of Molecular and Mic

Re: [gmx-users] Regarding downloading make_hole program

You should look at the GROMACS site, contribution. Cheers, Itamar - Original Message - From: "naga raju" <[EMAIL PROTECTED]> To: Sent: Friday, May 25, 2007 3:32 PM Subject: [gmx-users] Regarding downloading make_hole program Dear gmx users, would you tell

Re: [gmx-users] energy minimization - double precision

Hi, When doing EM it is not a good idea to use restrains/constraints when doing EM. Try minimize without it. Best, Itamar --- "Prediction is very difficult, especially about the future" - Niels Bohr === | Itamar Kass, Ph.D. | Postdoctora

Re: [gmx-users] Visualization Problem

ch before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- "Prediction is very difficult, especially about the future" - Niels Bohr ===

Re: [gmx-users] rotational fit in XY plane only

t in XY plane only Well, you can ofcourse run trjconv twice... Tsjerk On 5/3/07, Itamar Kass <[EMAIL PROTECTED]> wrote: Dear Berk, Thanks you very much for your quick and helpfully replay. If I may be a bit nudnik and ask to get it as "rotxy+transxyz" instated of "ro

Re: [gmx-users] rotational fit in XY plane only

; <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: RE: [gmx-users] rotational fit in XY plane only Date: Wed, 02 May 2007 14:10:59 +0200 From: Dr Itamar Kass <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Discussion l

[gmx-users] rotational fit in XY plane only

of doing so? Best, Itamar --- "Prediction is very difficult, especially about the future" - Niels Bohr === | Itamar Kass, Ph.D. | Postdoctoral Research Fellow | |Molecular Dynamics Group | School of Molecular and Microbial Sciences (SMMS) |

[gmx-users] overcome the integration problem (installing CVS)

First, the GROMACS site is down now. Second from the bit I have read, it is not clear to me how to install the stable CVS and not an experimentally version. Best, Itamar --- "Prediction is very difficult, especially about the future" - Niels Bohr =======

Re: [gmx-users] PME, epsilon_rf and dielectric constant calculation

ibe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- "Prediction is very difficult, especially about the future" - Niels Bohr === | Itamar Kass

[gmx-users] PME, epsilon_rf and dielectric constant calculation

Dear all, I wish to calculate the dielectric constant of small molecules liquids. In order to do so, I am simulating the system using PME, with epsilon_r = 1. I have few questions: 1. What is the meaning of epsilon_rf when I am using PME, if it important, what it should be? 2.

Re: [gmx-users] NVT with lipid bilayer

Justin Lemkul wrote: > Hello all, > > I'm having a few more problems running an NVT ensemble on my system. I have an > integral membrane protein, with a transmembrane helix and small extracellular > domain. The bilayer is DPPC. I have one face of the bilayer solvated to > surround the extracellu

[gmx-users] conversion gromos gromacs

Hi, I need to convert GROMOS topology file into GROMACS format, I wonder if someone know of a program in GROMACS or GROMOS packages that does it. Thanks, Itamar -- "Prediction is very difficult, especially about the future" - Niels Bohr ___ gmx-user

Re: [gmx-users] Extent of data transfer between nodes

Shalom Berk, The reseaon I wish to know is that my system administrator asked me for this data. What I need is a rough assessment. Thanks, Itamar Berk Hess wrote: From: Itamar Kass <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: Gromax user group Subject

[gmx-users] Extent of data transfer between nodes

Hi all, I wonder if someone can estimate the number of MPI calls/sec and Mbytes/sec transferred when using GROMACS 3.3.1 to simulate a system of ~25K atoms? Thanks, Itamar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/

Re: [gmx-users] why the mdrun stop

> your friend > > === | Itamar Kass | The Alexander Silberman | Institute of Life Sciences | Department of Biological Chemistry | The Hebrew University, Givat-Ram | Jerusalem, 91904, Israel | Tel: +972-(0)2-6585194 | Fax: +

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