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

-- 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

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

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 Research Fellow | | Department of Biochemistry and Molecular Biology | Building 77

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

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 1/09/2011 6:32 PM, Itamar Kass wrote: Hi

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 itamar.k...@monash.edu wrote: Hi

Re: [gmx-users] Simulation of a crystal

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. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar Kass

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

. 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 itamar.k...@monash.edu wrote: HI Chris, I am sorry that from my mails it is seems like I am not appreciate the help, because I appreciate it much

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

, 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 | Wellington

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

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

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

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 end with the same results. I didn't try

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

A. Lemkul wrote: Itamar Kass wrote: Hi Mark, I didn't had the time to do the SD yet, but serial run end with the same results. I didn't try water only system, as this is of no interest to me, but I will simplify the system later on. Being of interest to you and being a useful diagnostic

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

-compiled binary. What error messages do you get when the crash occurs? On Tue, Aug 16, 2011 at 9:48 PM, Itamar Kass itamar.k...@monash.edu wrote: Hi all GROMACS useres and developers, I am interesting in simulating a small protein (~140 aa) in water, with and without Ca ions. In order

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

cluster/blue-gene. cheers, Itamar On 18 August 2011 01:48, Matthew Zwier mczwier at gmail.com 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 itamar.kass at monash.edu

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, On 18/08/2011, at 9:36 AM, Justin

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

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

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

Zwier mczwier at gmail.com 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 itamar.kass at monash.edu wrote: Hi all GROMACS useres and developers, I am interesting

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

, 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 | Wellington

Re: [gmx-users] Simulation a labeled protein

field? If there is someone who has experiences in such systems, please have some advice. Thanks in advance, Faezeh -- In theory, there is no difference between theory and practice. But, in practice, there is. - Jan L.A. van de Snepscheut === | Itamar

[gmx-users] malloc on mac

=== | 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] maintained an Hbond using a distance restraint

. 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 | Australia

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

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 am using a distance

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 validity

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

. 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 9902 9376 | Fax: +61 3

Re: [gmx-users] dealing with ATP

, 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

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

=== | 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] No cut-off

, 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

Re: [gmx-users] Protein-membrane system

, 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 | Wellington Road

Re: [gmx-users] General MD question

-- -- 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 Campus

Re: [gmx-users] transmembrane protein simulation

-- 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

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

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 9902 9376 | Fax

Re: [gmx-users] dna, lipid simulation

=== | 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] Problems when simulating a protein in its crystal matrix.

, 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 | Wellington Road | Monash

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

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

Re: [gmx-users] g_cluster cutoff

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

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 Molecular Biology

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 itamar.k...@monash.edu Date: Monday, September 6, 2010 14:06 Subject: [gmx-users] Protein stability using MARTINI

[gmx-users] Protein stability using MARTINI

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. | Postdoctoral

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

(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. | Postdoctoral Research Fellow

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 Biochemistry and Molecular

Re: [gmx-users] rmsd between different monomers

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

[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 | Building 77 Clayton

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 Molecular Biology

[gmx-users] indexing and new molecules

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] indexing and new molecules

=== | 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

[gmx-users] g_cluster group for output

. 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 | Australia

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

[gmx-users] atomnumber=-12345

. 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] atomnumber=-12345

...@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 11:13 AM

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 chihying2...@gmail.comwrote: Hi 6LYZ.pdb is simply a lysozyme structure and I merely solvated it

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

Re: [gmx-users] pdb2gmx -missing

Hi, Try to use -ignh. On Wed, Nov 11, 2009 at 7:09 PM, leila karami karami.lei...@gmail.com 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

Re: [gmx-users] pdb2gmx -missing

them even further from solving their problems. Cheers, Tsjerk On Wed, Nov 11, 2009 at 9:16 AM, Itamar Kass itamar.k...@gmail.com wrote: Hi, Try to use -ignh. On Wed, Nov 11, 2009 at 7:09 PM, leila karami karami.lei...@gmail.com wrote: I do command pdb2gmx but follow warning and error

[gmx-users] solvation energy calculation

, 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

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

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 m.ekram...@ph.iut.ac.irwrote: Hi Mark my mdrun command line is : mpirun -n 4 mdrun_mpi -v -s topol.tpr regards -- Milad Ekramnia Physics

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: [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

[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

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 mark.abra...@anu.edu.auwrote: 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] *** Process received signal *** [xn068

[gmx-users] run g_cover in parallel

=== | 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

Re: [gmx-users] run g_cover in parallel

there are more parallel things then just MD. Cheers, Itamar On Wed, Oct 14, 2009 at 10:48 AM, Mark Abraham mark.abra...@anu.edu.au wrote: Itamar Kass wrote: Hi, I wonder if there a way to run g_cover in paralel in order to make things run faster? No. Obviously you can use -dt to reduce

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

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

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

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 itamar.k...@gmail.com mailto:itamar.k

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

. 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 | Australia

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 .

[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 Research Fellow | | Department

[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 | | Department

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

=== | 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

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 Bhattacharyasamikb...@yahoo.co.in wrote: hi i'm simulating a ion channel protein

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 inons...@tau.ac.il wrote: Hi everyone! I'm

[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

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

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 Group

[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

Re: [gmx-users] Extending MD run

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 md.mdp -c MD1

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

, 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 --with-fft=fftw2 make -j 2

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

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 has problems with the intel one

[gmx-users] errores during compilation of GROMACS 3.3.2

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 and Microbial Sciences (SMMS

Re: [gmx-users] simulation popc

! 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 === | Itamar

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

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

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 Microbial Sciences (SMMS

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: gmx-users@gromacs.org Sent: Friday, May 25, 2007 3:32 PM Subject: [gmx-users] Regarding downloading make_hole program Dear gmx users,

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. | Postdoctoral Research Fellow

Re: [gmx-users] Visualization Problem

)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 === | Itamar Kass, Ph.D

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

list for GROMACS users gmx-users@gromacs.org 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 gmx-users@gromacs.org To: Discussion list

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

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 rotxy+transxy thats will be wonderfully

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

, 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 === | Itamar Kass, Ph.D

[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] PME, epsilon_rf and dielectric constant calculation

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 | Postdoctoral Research Fellow

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 extracellular

[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-users

[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

Re: [gmx-users] why the mdrun stop

=== | 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: +972-(0)2-6584329 | Email: [EMAIL PROTECTED

Re: [gmx-users] protein in bilayer

the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- === | Itamar Kass | The Alexander Silberman | Institute of Life Sciences | Department of Biological Chemistry | The Hebrew University

Re: [gmx-users] editconf

@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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 -- === | Itamar Kass

[gmx-users] GROMACS on Ubunto

denied mknod: `dm': Permission denied mknod: `dm': Permission denied mdadm: /dev/md-v not identified in config file. Any ideas anyone? Best, Itamar. -- === | Itamar Kass | The Alexander Silberman | Institute of Life Sciences | Department of Biological

Re: [gmx-users] GROMACS on Ubunto

And that means? Or better, how do I overcome it? Itamar. David van der Spoel wrote: Itamar Kass wrote: Shalom all, I am trying to install GROMACS 3.3.1 on my Ubuntu/dapper machine. The installation is OK, and pdb2gmx as well as grompp are OK also. Still, when I try to run mdrun I got

Re: [gmx-users] popc

Shalom, Try make_hole.pl -f input.pdb -o output.pdb -r 1.2 -lipat P -lipid POP Itamar P.S. look at the pdb file for the atom name of the phosphate atom. I use DMPC so it is P, but it is also might be P8 or such. MGiò wrote: Ooops! I mean, I'm using popc.itp, of course! bye, MG On

Re: [gmx-users] Fw: TM protein, lipids, force field

types for the DPPC molecules? Thank you for your help. All the best. === | Itamar Kass | The Alexander Silberman | Institute of Life Sciences | Department of Biological Chemistry | The Hebrew University, Givat-Ram | Jerusalem, 91904, Israel | Tel: +972

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