Re: [gmx-users] DSSP-last GROMACS 4.5.7 can not use DSSP -please help to solve it

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Re: [gmx-users] how to optimize the orientation of the protein in a dodecahedron

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Re: [gmx-users] a question about ensemble

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Re: [gmx-users] citation for pdb2gmx -vsite hydrogens

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Re: [gmx-users] Getting local pressure

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Re: [gmx-users] system cooling down when runing NVE

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Re: [gmx-users] Calculation of solvent and solute relaxation times

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Re: [gmx-users] movement in 2 directions - remove one degree of freedom

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Re: [gmx-users] What is the autocorrelation time

it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688

Re: [gmx-users] Pressure at constant volume

--- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx

Re: [gmx-users] How to over come syntax errors

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Re: [gmx-users] Fwd: How to overcome syntax errors

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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology

Re: [gmx-users] intermolecular H bond selection

--- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html

Re: [gmx-users] What is the autocorrelation time

) events, or in other words to poor sampling? Intuitively, I'd say that the interpretation of the acf (at least for the decay and the decorelation) is always valid unless maybe if you have very poor statistics. Ciao, Patrick Le 20/05/2012 16:12, Erik Marklund a écrit : Dear Chris, As I

Re: [gmx-users] Simulation protocol for Protein-DNA-complex

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Re: [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond

/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab

Re: [gmx-users] MD Training

interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18

Re: [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond

and the charge of the key atoms (of course for hydrogen bond no charge are involved). Cheers, Acoot From: Erik Marklund er...@xray.bmc.uu.se To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Sunday, 3 June 2012 6:18 PM Subject: Re: [gmx-users] Re : How GROMACS calculate

Re: [gmx-users] Writing and compiling new analyses for gromacs

--- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing

Re: [gmx-users] Trajectories

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Re: [gmx-users] Trajectories

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Re: [gmx-users] Regarding error.

--- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users

Re: [gmx-users] Bonds and atom-pairs in g_hbond

--- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list

Re: [gmx-users] dodssp segmentation fault SOLVED for DEBIAN

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Re: [gmx-users] multi-chain pdbs with mdrun?

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Re: [gmx-users] protein near the edges of simulation box

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[gmx-users] Numbering for pbc_atom0

? Best, --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html

Re: [gmx-users] Numbering for pbc_atom0

Nevermind. I figured it out I think. It was more of a problem with box size. Erik 15 jun 2012 kl. 14.20 skrev Erik Marklund: Hi users, I am seeing some unexpected behavior for my COM pulling simulations. Errors arise from the COM and distance calculations and I reckon it can be fixed

Re: [gmx-users] specifying the direction of Pull in US

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Re: [gmx-users] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond

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Re: [gmx-users] Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond

/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab

Re: [gmx-users] g_rms and g_rmsdist on initial structure

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Re: [gmx-users] Re: g_rms and g_rmsdist on initial structure

. They are exactly the same. So I don't understand why g_rms(g_rmsdist) selecting group C-alpha give me high values. Sincerely yours, Hsin-Lin Erik Marklund wrote Hi, Since gromos-forcefields are not strictly all-atom forcefields, there might be a mismatch between atoms in the two

Re: [gmx-users] Topology- make bonds with certain cut-off distance

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Re: [gmx-users] deltaG from PMF

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Re: [gmx-users] deltaG from PMF

window takes around a week on 12 cpus. I think that neglecting first 20 ns would be the best. The penalty is app 0.5 kcal/mol at this time so really good. On Tue, Aug 28, 2012 at 3:28 PM, Erik Marklund er...@xray.bmc.uu.se wrote: I would simulate longer. What are the autocorrelation times

Re: [gmx-users] deltaG from PMF

to e.g. 10. On Tue, Aug 28, 2012 at 4:19 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Indeed, extended simulations are always painful. Nevertheless, g_wham calculates the autocorrelations and use them for producing more accurate error estimates. They can also give a hint about wether you

Re: [gmx-users] building_insertion_mutants

the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden

Re: [gmx-users] Re: Turning off electrostatics between groups using custom tables?

-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18

Re: [gmx-users] Effect of refcoord_scaling

it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688

Re: [gmx-users] Rotated protein

--- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users

Re: [gmx-users] charge calculation........

-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688

Re: [gmx-users] Extracting bond information from topol.tpr file using template.c

/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab

Re: [gmx-users] select randomly some of my moleculesand replace them,

://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se

Re: [gmx-users] energy minimization output

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 --- Erik Marklund, PhD Dept. of Cell and Molecular

Re: [gmx-users] energy minimization output

proceed with NPT if the system is not in equilibrium? On Wed, Sep 26, 2012 at 1:11 PM, Erik Marklund er...@xray.bmc.uu.se wrote: 26 sep 2012 kl. 08.16 skrev Shima Arasteh: Dear all, My system contains lipids, protein and water. I want to energy minimize it, so ran grompp: # grompp -f

Re: [gmx-users] Re: distance restraint

http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http

Re: [gmx-users] DNA orientation restrain

the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden

Re: [gmx-users] Re: DNA orientation restrain

--- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list

Re: [gmx-users] generation of .itp file

--- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list

Re: [gmx-users] Re: pull=constraint gives zero forces

://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2

Re: [gmx-users] Installing an Individual Tool (g_select)

...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755

Re: [gmx-users] Regarding Gromacs output files.

/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 --- Erik Marklund

Re: AW: [gmx-users] question about the minimization

or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18

Re: [gmx-users] Fwd: I have a symmetric simulation box,

/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab

Re: AW: [gmx-users] question about the minimization

it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688

Re: [gmx-users] Extending simulation

--- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx

Re: [gmx-users] Segmentation fault while calculating water mediated H-bond with g_hbond

post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er

Re: [gmx-users] Center of my simulation box

...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755

Re: [gmx-users] Can't center box with trjconv

/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab

Re: [gmx-users] fraction of native contacts calculation

/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio

Re: [gmx-users] Protein at given pH

http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http

Re: [gmx-users] Protein at given pH

7 nov 2012 kl. 16.21 skrev Steven Neumann: On Wed, Nov 7, 2012 at 2:55 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, I've used the H++ server myself at times. My experience is that it's rather sensitive to the very fine detail of the input structure in some cases. I've had

Re: [gmx-users] Running Gromacs in Clusters

...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511

Re: [gmx-users] Running Gromacs in Clusters

/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab

Re: [gmx-users] Running Gromacs in Clusters

--- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Running Gromacs in Clusters

, Erik Marklund er...@xray.bmc.uu.se wrote: Hi, Sure you can go beyond 24 cores. I'm currently simulating ~170 000 atoms on 192 cores at ~45 ns a day. with half the number of processors I get ~27 ns a day. It will of course depend on the hardware, particular algorithms, run parameters

Re: [gmx-users] REMD with Frozen DNA and Moving Protein

)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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3

Re: [gmx-users] rigid structure

--- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing

Re: [gmx-users] problem with simulation of freezing of water

--- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx

Re: [gmx-users] do_dssp Segmentation fault

/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab

Re: [gmx-users] calculating lennard-jones interaction

/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio

Re: [gmx-users] calculating lennard-jones interaction

, and in the other case the distance between two proteins is less than the cut off value, Bests -Zahra From: Erik Marklund er...@xray.bmc.uu.se To: Zahra M s_zahra_mous...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, November 13, 2012 2:08 PM Subject

Re: [gmx-users] amino acid color

post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se

Re: [gmx-users] Re: Umbrella sampling question

--- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list

Re: [gmx-users] Dihedral form

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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University

Re: [gmx-users] Dihedral form

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Erik Marklund [er...@xray.bmc.uu.se] Sent: 15 November 2012 13:37 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Dihedral form You could shift the reference angle

Re: [gmx-users] Re: Umbrella sampling question

the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden

Re: [gmx-users] Force vs distance plot in pulling simulation?

is to write a simple script that parses out the columns you want. -Justin I don't see the point though. Except for checking implementation of the pull code. --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3

Re: [gmx-users] Save frames of trajectory file

/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html

Re: [gmx-users] how to repeat simulation correctly?

://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 --- Erik

Re: [gmx-users] how to repeat simulation correctly?

the outcome of starting several trajectories from the same equilibrated frame as continuation runs, i.e., using its velocities? Could they be considered independent and used to extract that valuable statistics mentioned in a previous posting? Felipe On 11/22/2012 10:04 AM, Erik Marklund

Re: [gmx-users] how to repeat simulation correctly?

10:04 AM, Erik Marklund wrote: Stochastic and chaotic are not identical. Chaotic means that differences in the initial state will grow exponentially over time. Erik 22 nov 2012 kl. 09.52 skrev Felipe Pineda, PhD: Won't this same stochastic nature of MD provide for different

Re: [gmx-users] Hbonds between Adenine and Thymine

)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 --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3

Re: [gmx-users] Observations about g_hbond -dist and -ang

/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio

Re: [gmx-users] Asymmetry in homo dimer simulation

? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er...@xray.bmc.uu.se

Re: [gmx-users] merge .gro, .top files

post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 6688fax: +46 18 511 755 er

Re: [gmx-users] using g_analyze for calculating distance autocorrelation functions

the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --- Erik Marklund, PhD Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala

Re: [gmx-users] mdp option for implicit solvent simulation

Hi, If you're simulating in the gas-phase, how come you want implicit solvent? Erik On Jan 11, 2013, at 5:07 AM, Sanku M wrote: Hi, I am trying to do implicit solvent simulation for a protein in gas- phase. I have a few questions : 1) should I use sd integrator? 2) should I also use

Re: [gmx-users] Hydrogen bonding differences

Hi. What version was this? Have you tried with -nomerge? Erik On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote: Dear users, While calculating hydrogen bonds for a simulation, it was found that the average number of intra protein hbonds was not equal to sum of MM, MS and SS hydrogen bonds.

Re: [gmx-users] how can I make statics for Z-axis?

g_traj -nox -noy if I recall correctly. On Jan 21, 2013, at 4:10 PM, Albert wrote: hello: I would like to make statics for an atom along Z-axis. I am just wondering how can I to do this in Gromacs? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] RMSD

On Jan 25, 2013, at 5:53 AM, Shima Arasteh wrote: Thanks for your reply. I want to chose one of the 5 conformers from a NMR PDB. As I studied in literature, the average structure could be selected regarding RMSD values and the go on with selected one to simulate in in water, lipid

Re: [gmx-users] Hydrogen bonding differences

, Erik Marklund er...@xray.bmc.uu.se wrote: Hi. What version was this? Have you tried with -nomerge? Erik On Jan 21, 2013, at 10:55 AM, Kavyashree M wrote: Dear users, While calculating hydrogen bonds for a simulation, it was found that the average number of intra protein hbonds

Re: [gmx-users] Visualize Protein ligand complex after simulation

Short answer is to inspect your complex with VMD or Pymol (or some other viewer). Pymol takes pdb input, so unless your structure is contained in a pdb file you must convert it with e.g. trjconv first. If you want a single frame you need to extract one form your trajectory, or, if the

Re: [gmx-users] Dynamics of the salt-bridges

Hi, If you don't care about the exact distances, but rather the time the groups spend within a certain distance, g_hbond -contact can be useful. Best, Erik On Feb 3, 2013, at 6:36 PM, James Starlight wrote: Justin, 1 )for example I want to select in index file only all asp, glu and his

Re: [gmx-users] How to analysis 10 ns from 20 ns simulation

HI, It should read trjconv. And all analysis tools have the -b and -e flags for excluding the start or the end of a trajectory. Erik On Feb 4, 2013, at 7:00 AM, Emanuel Birru wrote: Use trajconv http://manual.gromacs.org/online/trjconv.html -Original Message- From:

Re: [gmx-users] Regarding manual velocity generation in simulation

On Feb 5, 2013, at 8:22 AM, bipin singh wrote: Hello All, Please let me know whether is it possible to manually assign the velocity for each atom in the simulation instead of generating through gen_vel option. If the preceision of a gro-file is sufficient you can use such for manually

Re: [gmx-users] The time for the temperature and pressure coupling

Hi, Perhaps a side point: Temperature and pressure can not be seen as constraints to the system at any given instant in the sense that e.g. the instantaneous kinetic energy perfectly match the temperature at every time step just because you have a thermostat. Time and ensemble averages

Re: [gmx-users] RNA MD

I've never seen good parameters for nucleic acids. There might be such, but none that ship with gromacs as far as I know. Erik On Feb 7, 2013, at 4:25 AM, 김현식 wrote: Dear experts, Hello! Is it possible to run RNA md with GBSA? Thank you. bestKim.

Re: [gmx-users] Calculation of the Force on the center of bonds

Try virtual sites constructions. On Feb 11, 2013, at 6:01 PM, Rasoul Nasiri wrote: Dear All, I need to define interaction sites on the center of C-H bonds instead of nuclei of each atom. The main reason was that non-bonding parameters (sigma and epsilon) have been parametrized in these

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