[gmx-users] Bilayer curvature

. Does anybody knows is it normal or something is wrong? Which factors do affect the membrane curvature (like: initial conf., water, ions, box size, equilibration steps, ...)? Thanks, Dariush -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] Re: oxidized lipid - Peroxidated lipid

Dear All, I need to use oxidized lipids in my system. Any suggestion for force field that I can use would be appreciated. Thanks, Dariush -- View this message in context: http://gromacs.5086.x6.nabble.com/oxidized-lipid-Peroxidated-lipid-tp5008661p5008810.html Sent from the GROMACS Users

[gmx-users] oxidized lipid - Peroxidated lipid

Hi All, Does anybody know which force filed I can use for oxidized lipid or peroxidated lipid? You can see the below link to get how fatty acid will change by peroxidation: http://en.wikipedia.org/wiki/Lipid_peroxidation If there is not any, what is the suggestion? Thanks, Dariush -- View

[gmx-users] arrange the atoms in sphere

Hello All, Does anybody have any script to arrange the molecules in the sphere? Actually, I need to set up a LDL (has hydrophobic core and monolayer of PC around). Thanks, Dariush -- View this message in context: http://gromacs.5086.x6.nabble.com/arrange-the-atoms-in-sphere-tp5008599.html

[gmx-users] Re: atom numbering

Thank you dear Justin! Dariush On Fri, Aug 17, 2012 at 11:04 AM, Justin Lemkul [via GROMACS] < ml-node+s5086n5000298...@n6.nabble.com> wrote: > > > On 8/17/12 10:41 AM, dariush wrote: > > genconf -renumber works well for renumbering. However, after > minimization >

[gmx-users] Re: atom numbering

genconf -renumber works well for renumbering. However, after minimization of that renumbered .gro file, I have previous numbering. Dariush On Thu, Aug 16, 2012 at 5:54 PM, Justin Lemkul [via GROMACS] < ml-node+s5086n5000267...@n6.nabble.com> wrote: > > > On 8/16/12 5:22 PM

[gmx-users] atom numbering

protein 2. Do you know how should I figure it out? Thanks, Dariush -- View this message in context: http://gromacs.5086.n6.nabble.com/atom-numbering-tp5000266.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] PMF - Protein-Me​brane

them and calculate the PMF? What would be the difference? Thanks, Dariush -- View this message in context: http://gromacs.5086.n6.nabble.com/PMF-Protein-Me-brane-tp569.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users

[gmx-users] Boundary

movie in VMD, even you add some mirror-wise molecule in each direction. Is there anyway to figure out this problem? Thanks, Dariush -- View this message in context: http://gromacs.5086.n6.nabble.com/Boundary-tp4999167.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com

[gmx-users] Simple question (confout)

the box. PS: It does not matter either NPT or NVT was used. Thanks, Dariush -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't

Re: [gmx-users] MARTINI parameters for dodecyl maltoside (DDM)

Sure, this is the way to make forcefield for your molecule. Also, please check literature. Good luck, Dariush On Mon, May 21, 2012 at 9:26 AM, francesco oteri wrote: > Hi Dariush, > I've checked but it seems there no parameters for my detergent. > > Actully there are paramet

Re: [gmx-users] MARTINI parameters for dodecyl maltoside (DDM)

Have you checked MARTINI website? http://md.chem.rug.nl/cgmartini/index.php/downloads/force-field-parameters Dariush Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA

[gmx-users] fly some lipids to water

cardiolipin) fly away from bilayer and come inside the water. Does anybody know what is the problem? How should I fix my system? I am using Coarse grained model using MARTINI force field. Thanks, Dariush -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of

Re: [gmx-users] Position Restraints

Thanks dear Justin. No, the protein is moving in right direction, but I am going to restrain any changing the position and then monitory these movements during MD run. I could see the Pos. Res. works in md.log file. Regards, Dariush On Thu, Apr 26, 2012 at 1:38 PM, Justin A. Lemkul wrote

[gmx-users] Position Restraints

this kind of movements? Regards, Dariush -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list

Re: [gmx-users] About Distance.pl script

I have gotten this error previously. I changed the address of the g_dist (e.g. /user/gromacs/bin/g_dist) in distances.pl file and it works. Dariush On Thu, Mar 29, 2012 at 11:51 AM, vidhya sankar wrote: > Dear justin , Thank you for your previous reply > When i Download and run Dista

Re: [gmx-users] Box Size in MD

As far as I concern, the minimum size is that cove all parts of your molecules or system. In case you should use solvent it is up to you to add how many molecules and in this case you should make decision by experience or according to literature. Dariush -- Kind Regards, Dariush Mohammadyani

Re: [gmx-users] clashes

ation"? Thanks, Dariush On Wed, Mar 14, 2012 at 10:08 AM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> Dear user, >> When I am using: >> genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro >> to add water in

[gmx-users] clashes

figure it out? Or actually if we have some clashes in system how we can correct them? Thanks, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA -- gmx-users mailing list

Re: [gmx-users] Martini

I think I made a mistake: Aniline: SC4 -SC4 - SNd Pyrrole: SC4 -SNd Tiofen: SC4 - SC5 I am not sure... On Thu, Mar 8, 2012 at 3:24 PM, dina dusti wrote: > Dear Dariush, > > Thank you very much from your response. > Then you tell me that the definition of aniline and pyrrole

Re: [gmx-users] Martini

SC5 does not work? Dariush -- Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501 Fifth Avenue Pittsburgh, PA 15261 USA On Thu, Mar 8, 2012 at 2:34 PM, dina dusti wrote: > Dear Gromacs Speciali

Re: [gmx-users] NAMD file (.inp) convert to GROMACS format

Thanks Justin! There is one script in User Contributions page, but it does not work. I totally changed my way, I will use NAMD in this case... On Fri, Jan 27, 2012 at 2:11 PM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> Is there any similar script to

Re: [gmx-users] NAMD file (.inp) convert to GROMACS format

Is there any similar script to change it for this reason? On Fri, Jan 27, 2012 at 11:26 AM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> Hi all, >> >> I have two files (Topology and Parameter files) in NAMD format (*.inp). I >> am going to

[gmx-users] NAMD file (.inp) convert to GROMACS format

Hi all, I have two files (Topology and Parameter files) in NAMD format (*.inp). I am going to use them in GROMACS. Can you help me how can I use them? Kind Regards, Dariush Mohammadyani Department of Structural Biology University of Pittsburgh School of Medicine Biomedical Science Tower 3 3501

Re: [gmx-users] Cytochrom C

GROMACS 4.5.3 and charmm27.ff. Cytochrome C is a difficult protein to simulate :( Thanks, Dariush On Tue, Jan 17, 2012 at 10:33 AM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> According your help and "pdb2gmx -his -missing" I could create input

Re: [gmx-users] Cytochrom C

According your help and "pdb2gmx -his -missing" I could create input files. Also I used grompp without error. However, for mdrun I got this error: *Function type CMAP Dih. not implemented in ip_pert* How can I figure it out? Thanks, Dariush On Tue, Jan 10, 2012 at 4:37 PM, Krzyszt

[gmx-users] Coarse Grained Cytochrom C

Hi all, Has anybody used Coarse grained model for Cytochrome C? I could create a model using MARTINI forcefiels (using martinize.py script and 1HRC.pdb file), but it does not have HEM and HOH groups. Can anybody help me? Kind Regards, Dariush Mohammadyani Department of Structural Biology

Re: [gmx-users] Cytochrom C

Dear Justin, I could not find HIS in CHARMM and GROMOS53a6. Somebodies offer to rename it to HSE or HSD, but I do not know why? and which one is correct. I am working on Cytochorom c. Thanks, Dariush On Tue, Jan 10, 2012 at 4:22 PM, Justin A. Lemkul wrote: > > > Dariush Mohammady

Re: [gmx-users] Cytochrom C

Does anybody know where can I find [ HIS ] parameters? Thanks, Dariush On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani < d.mohammady...@gmail.com> wrote: > Dear Peter and Krzyszto, > > Thank you. I am following your comments. If I get any problem I will come > back. >

Re: [gmx-users] umbrella sampling tutorial quastion

As I know, it is not necessary to restrain neither reference nor pulled group. When you apply pulling force, it means you have restrained both of them. Dariush On Mon, Jan 9, 2012 at 4:15 PM, przemek bartha wrote: > Hello, > According to Justin's tutorial on umbrella sampling, >

Re: [gmx-users] Cytochrom C

gt; > > OO -0.515 > > >[ bonds ] > > > CH3HH31 > > > CH3HH32 > > > CH3HH33 > > > CH3C > > > C O > > > > > > Surprisingly, an .hdb entry for

Re: [gmx-users] Cytochrom C

I tried charmm27 too. Error: Residue 'ACE' not found in residue topology database I tried all forcefield in the list provided by "pdb2gmx", but non of them works. Dariush On Thu, Jan 5, 2012 at 1:42 PM, Robert Hamers wrote: >HEME is in the charmm27 force field. &g

Re: [gmx-users] RDF(PMF) and Umbrella sampling

Hi Gavin, A question arose for me: why did you consider the (rate = 0)? Dariush On Fri, Jan 6, 2012 at 11:47 AM, Gavin Melaugh wrote: > Hi Justin > > Just a quick clarification regarding my previous point. With geometry = > distance, and pull_dim =Y Y Y . Is the pull_group

Re: [gmx-users] Cytochrom C

heir website; I used martinize.py script; Again I got error. Regards, Dariush On Thu, Jan 5, 2012 at 11:51 AM, Justin A. Lemkul wrote: > > > Dariush Mohammadyani wrote: > >> >> Hi all, >> >> Has anybody made initial configuration for Cytochrom C? Can it be

[gmx-users] Cytochrom C

Hi all, Has anybody made initial configuration for Cytochrom C? Can it be shared with me? Thanks, Dariush -- 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