Re: [gmx-users] Distance restraints

Hi..,Mark but it is within the same molecule , not in inter-molecules. On Tue, May 21, 2013 at 11:36 AM, Mark Abraham mark.j.abra...@gmail.comwrote: Yes. Check out the manual first! Mark On Tue, May 21, 2013 at 5:16 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: Hi Mark

Re: [gmx-users] Stimulation stopped at 2ns

: On 7/8/13 4:33 PM, Rama wrote: Dear All, I'm trying to do long stimulation run but every time it stops at 2ns, below pasted .mdp file parameters. How to run 10ns or more ns stimulation run? Do I need to change any parameters in .mdp file or else where. There is nothing in the .mdp file

Re: [gmx-users] snapshot

-dump 0 -sep Thanks in Advance. Rama On Mon, Jul 15, 2013 at 2:02 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: look for either -dt or -skip. Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 2:03 AM, Rama ramkishn...@gmail.com wrote: Hi, How to get a snapshots in equal intervals

Re: [gmx-users] snapshot

Thank you very much *Justin*. -- Rama On Mon, Jul 15, 2013 at 8:06 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 9:02 AM, Rama Krishna Koppisetti wrote: Hi, The following command I used for the snapshots but I'm getting one frame time 0 time 500. what are the changes I need

Re: [gmx-users] Re: snapshot

Thanks *Thomas* --Rama On Mon, Jul 15, 2013 at 9:00 AM, Thomas Schlesier schl...@uni-mainz.dewrote: Hi, the following: trjconv -s md.tpr -f md.trr -o beta.gro -dt 250 -sep should work. -dt 250 ; write output every 250 ps -sep ; to write each frame (but the output frequency gets

Re: [gmx-users] How to make changes on Trajectory file?

O kay... T hanks for prompt reply *Justin* * . --Rama ** * On Mon, Jul 15, 2013 at 11:11 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 12:08 PM, Rama wrote: Hi, I saved my coordinates every 500ps in production MD run, could I alter now .xtc file by saving different coordinates

Re: [gmx-users] NMR restrained MD

1.0 14258216 1 8 1 0.0 1.52462.0791.0 On Fri, Sep 6, 2013 at 4:23 PM, Rama ramkishn...@gmail.com wrote: Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data. Without

Re: [gmx-users] NMR restrained MD

H i Justin, Thanks for your reply. How to do that? On Fri, Sep 6, 2013 at 4:27 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:23 PM, Rama wrote: Hi, I'm doing NMR restrained MD simulation for protein-Bilayer system to satisfy NMR experimental data. Without restraints

Re: [gmx-users] NMR restrained MD

Hi Justin , Is there any script available in gromacs documentation or some where? Thanks On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote: H i Justin, Thanks for your reply. How to do that? If .rtp entries

Re: [gmx-users] NMR restrained MD

Hi Justin, I use similar procedure as you mentioned in the tutorial to generate my topologies for protein and bilayer. there is no .rtp file for lipid. Is there any reference to include lipid molecule in aminoacid.rtp file. Thanks Rama On Fri, Sep 6, 2013 at 4:57 PM, Justin Lemkul jalem

Re: [gmx-users] NMR restrained MD

Hi Justin, If you are willing to see my complex pdb file or complex .gro file and topology files, I'll send you for the reference. Thanks Rama On Sat, Sep 7, 2013 at 5:42 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/7/13 6:40 PM, Rama Krishna Koppisetti wrote: Hi Justin, I use

Re: [gmx-users] NMR restrained MD

Ok..I got it Thanks Justin... --Rama On Mon, Sep 9, 2013 at 1:49 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: Hi Justin , I prepared .rtp files for lipid. what is the exact command to merge two chains in gromacs. On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem

Re: [gmx-users] NMR restrained MD

Hi Justin , I prepared .rtp files for lipid. what is the exact command to merge two chains in gromacs. On Fri, Sep 6, 2013 at 4:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/6/13 5:35 PM, Rama Krishna Koppisetti wrote: H i Justin, Thanks for your reply. How to do

Re: [gmx-users] NMR restrained MD

Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters in the file .rtp. Thanks --Rama On Mon, Sep 9, 2013 at 4:43 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 5:37 PM, Rama Krishna Koppisetti wrote: Hi Justin, I merge two

Re: [gmx-users] NMR restrained MD

Hi Justin, I merge two molecules as a single molecule type. Now I'm trying to do energy minimization of the system, getting errors like Fatal error: [file topol.top, line 55130]: No default Proper Dih. types Any idea for this type of errors. Thanks --Rama On Mon, Sep 9, 2013 at 1:57

Re: [gmx-users] NMR restrained MD

, line 23515]: No default Ryckaert-Bell. types --Rama On Mon, Sep 9, 2013 at 5:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/9/13 6:11 PM, Rama Krishna Koppisetti wrote: Hi Justin, I included 1 DMPC molecule parameters in the file should I need to include 128 molecules parameters

Re: [gmx-users] NMR restrained MD

Hi Justin, It is which part in the force field. Exactly which file I have to look to overcome this errors. Thanks --Rama On Tue, Sep 10, 2013 at 8:25 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi Justin, This is another type of error

Re: [gmx-users] NMR restrained MD

several multiplicity terms. old: 0 5.09 2 0 5.09 2 new: LOSLP LOS LC21 0.00 3.193 Thanks --Rama On Tue, Sep 10, 2013 at 12:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 1:28 PM, Rafael I. Silverman y de la Vega wrote: Adding parameters can

Re: [gmx-users] NMR restrained MD

Hi, How to convert normal dihedrals to so-called Ryckaert-Bellemans potential dihedrals. Is there any script available for that. Thanks Rama On Tue, Sep 10, 2013 at 3:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 9/10/13 4:35 PM, Rama Krishna Koppisetti wrote: H i Justin, The force

Re: [gmx-users] NMR restrained MD

H i Justin, The force field that I constructed with OPLS + Berger lipids . Similar to your Bilayer tutorial. Thanks --Rama On Tue, Sep 10, 2013 at 3:26 PM, Rama Krishna Koppisetti ramkishn...@gmail.com wrote: -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

Re: [gmx-users] NMR restrained MD

Hi Justin, Should I use R-B dihedrals for DMPC lipids rather than periodic dihedrals. I'm getting an Error message like, ERROR 18815 [file topol.top, line 54180]: No default Ryckaert-Bell. types ERROR 18816 [file topol.top, line 54181]: No default Ryckaert-Bell. types --Rama

Re: [gmx-users] NMR restrained MD

LC2 LH11 0.00 3.773 LOS LC2 LH1 LC21 0.00 5.923 LC2 LH1 LOSLC1 0.00 3.773 T hanks Rama On Wed, Sep 11, 2013 at 8:17 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 9:05 AM, Rama Krishna Koppisetti wrote: Hi Justin

Re: [gmx-users] NMR restrained MD

Those lines are related to DMPC lipid dihedrals. -_Rama On Wed, Sep 11, 2013 at 8:17 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 9:05 AM, Rama Krishna Koppisetti wrote: Hi Justin, Should I use R-B dihedrals for DMPC lipids rather than periodic dihedrals. You should use

Re: [gmx-users] NMR restrained MD

Sorry.., Justin Yes.. It is a sequence of atom numbers from DMPC atoms. The errors are coming from all DMPC atoms dihedrals only not by protein dihedrals. --Rama On Wed, Sep 11, 2013 at 9:08 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/11/13 10:06 AM, Rama Krishna Koppisetti wrote

Re: [gmx-users] NMR restrained MD

--- I tried to look all the parameters in the .rtp file and ffbonded.itp and ffnonbonded.itp files I don't find any mistake. I hope you can help me --Thanks Rama On Wed, Sep 11, 2013 at 9:16

Re: [gmx-users] NMR restrained MD

: Incorrect number of parameters - found 3, expected 2 or 4 for Bond. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Thanks --Rama On Wed, Sep 11, 2013 at 6:47

Re: [gmx-users] NMR restrained MD

CC2 35.26 334.72 C1A OE OF C1B2 0.00 167.36 C2A OG OH C2B2 0.00 167.36 Thanks --Rama On Thu, Sep 12, 2013 at 8:28 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/12/13 9:21 AM, Rama Krishna Koppisetti wrote: Hi [ bondedtypes ] ; Col 1: Type

Re: [gmx-users] NMR restrained MD

) from starting residue PHE100 (Protein). Warning: Residue CA268 in chain has different type (Ion) from starting residue PHE100 (Protein). Thanks Justin .., I appreciate your help for whole week. I stopped here (give up). --Rama ___ Ramakrishna

Re: [gmx-users] NMR restrained MD

2520 2521 31 0.00 3.773 2519 2520 2521 2524 31 0.00 3.193 2519 2520 2521 2522 3 2519 2520 2521 2523 3 2520 2521 2524 2525 31 0.00 3.193 Thanks --Rama

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