[gmx-users] Gromacs 54a7 force field

Hi all... I heard that gromos 54a7 ff is much better for simulations than 53a6. i have a membrane protein system. To simulate it, should I include the berger lipid parameters manually as shown in justin Lemkul's membrane protein tutorial? Thanks -- View this message in context:

[gmx-users] Re: Gromacs 54a7 force field

54A7 also introduced changes to the Gromos96 lipid parameters How will this change my inclusion of the berger lipid parameters? Any thing that I should pay special attention to? Are there other lipid parameters more compatible? I heard from a faculty member at our Institute that the 53a6 is a bad

[gmx-users] Re: Gromacs 54a7 force field

Thanks for the quick and detailed replies Justin :) This helped clear some doubts I had. I thought all Charmm ff were compatible in Gromacs? Which Charmm ff were you referring to? -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-54a7-force-field-tp4999538p4999542.html

[gmx-users] Re: Gromacs 54a7 force field

So CHARMM36 would be the best ff for a long membrane protein simulation? Is it possible to integrate CHARMM36 into Gromacs? -- View this message in context: http://gromacs.5086.n6.nabble.com/Gromacs-54a7-force-field-tp4999538p4999544.html Sent from the GROMACS Users Forum mailing list archive at

[gmx-users] Re: Gromacs 54a7 force field

I got the answer to whether we can implement CHARMM36 into gromacs...:) thanks http://www.gromacs.org/Downloads/User_contributions/Force_fields I still want your opinion on whether it is the best ff for simulating a membrane-protein system, and if any modifications to the ff are necessary? Thanks

Re: [gmx-users] Re: Can i construct a solid wall in gromacs?

/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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13

Re: [gmx-users] g_bundle: angle with x or y axis.

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[gmx-users] Selectively choose the upper and lower leaflets of a DPPC bilayer.

Hi All, Is there a convenient method to selectively make an index file containing the upper leaflet and the lower leaflet of a DPPC bilayer? Thanks. -- View this message in context:

[gmx-users] g_density fails after calculating for the last snapshot

Hi All I have a 100 ns lipid simulation for which I want the density profile. I issued the following command g_density -f martin_md_290K_100ns_tau1.xtc -n dppc.ndx -s martin_md_290K_100ns_tau1.tpr -o water_density.xvg -b 5 The program fails with the following message Selected 3: 'Water'

[gmx-users] Re: g_density fails after calculating for the last snapshot

-send_instant_email%21nabble%3Aemail.naml -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- View this message in context: http://gromacs.5086.n6.nabble.com/g-density-fails-after-calculating

[gmx-users] G54a7 compatibility with G53a6?

Hi All I have a membrane protein with a lot of alpha helices in it. I want to use the 54a7 parameters for the protein and Kukol parameters (modified 53a6) for the POPC membrane. Is this feasible? I know that there are issues with combining widely different ffs, but these forcefields seem very

[gmx-users] Gromos 54A8 forcefield

Hi All, I just read the paper pertaining to Gromos 54A8. I was wondering if the force field files were available somewhere? Thanks. -- View this message in context: http://gromacs.5086.x6.nabble.com/Gromos-54A8-forcefield-tp5007713.html Sent from the GROMACS Users Forum mailing list archive

Re: [gmx-users] g_msd problem

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[gmx-users] g_wham error

)...can you please tell me how to correct this? Thanks -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] g_wham error

Oh lovely...thanks for the quick reply Justin :)... On Sat, Nov 19, 2011 at 10:57 PM, Justin A. Lemkul jalem...@vt.edu wrote: rajat desikan wrote: Hi I am a new gromacs user. I just completed Justin's umbrella sampling tutorial. I am doing a PMF calculation between 2 methane molecules

Re: [gmx-users] g_wham error

Justin, Should i turn off charges on the methane molecules? I have left them on. On Mon, Nov 21, 2011 at 12:32 AM, Justin A. Lemkul jalem...@vt.edu wrote: rajat desikan wrote: My simulations are for 10 ns in each window. There is a lot of noise in my wham too. I am enclosing my wham

Re: [gmx-users] g_wham error

)...does this have any bearing on my simulations? On Mon, Nov 21, 2011 at 3:05 AM, Justin A. Lemkul jalem...@vt.edu wrote: rajat desikan wrote: Justin, Should i turn off charges on the methane molecules? I have left them on. What force field are you using? If you've got an all-atom model

Re: [gmx-users] Simulation of the pure lipid bilayer

it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx

Re: [gmx-users] Re: MSD and frequency of writing trajectories

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Re: [gmx-users] Re: MSD and frequency of writing trajectories

to you. You can probably get creative with editconf's translation options and come up with some fake trajectories via trjcat that test some edge cases relevant to what you want to do. Mark On Wed, May 22, 2013 at 7:40 PM, rajat desikan rajatdesi...@gmail.com wrote: Hi Mark, Regarding

Re: [gmx-users] arrange the atoms in sphere

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Re: [gmx-users] GROMACS 4.6.2 released

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Re: [gmx-users] nvt T coupling group problem

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[gmx-users] Using the checkpoint file to restore corrupt trajectory.

Hi, I have a 20 ns long trajectory which has become corrupted beyond 18ns. I have the full checkpoint file. Is there any way I can use mdrun and the .cpt to rerun the simulation from 18ns and append it to the current .xtc (After I have clipped the part beyond 18ns by trjconv)? I did not find the

Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

Hi Justin, The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation will finish in one step. On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:38 AM, Rajat Desikan wrote: Hi, I have a 20 ns long trajectory which has become corrupted beyond

Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

. otherwise, I would have used the snapshot from 18ns and extended the simulation. Now, it looks like I will have to re-generate the velocities and re-equilibrate the system. On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan rajatdesi...@gmail.comwrote: Hi Justin, The checkpoint file has gone

Re: [gmx-users] Using the checkpoint file to restore corrupt trajectory.

Thank you! On Mon, Jul 15, 2013 at 6:29 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/15/13 8:56 AM, rajat desikan wrote: I guess, the more important question is whether the checkpoint file stores the previous checkpoints as well. If it stores only the last checkpoint at 20 ns, then I

Re: [gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1

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Re: [gmx-users] Force Field for peptides and proteins

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Re: [gmx-users] plans for mdrun features to deprecate in GROMACS 5.0

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Re: [gmx-users] Early registration period ending for 2013 GROMACS USA Workshop and Conference

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[gmx-users] rvdw, rlist and rcoulomb for Amber03

Hi Justin, In a recent post (http://gromacs.5086.x6.nabble.com/VDW-Cut-off-vs-Switch-with-CHARMM-force-field-td5010695.html;cid=1377399737789-944) you commented that: Unless you can demonstrate that your changes in cutoffs do not produce artifacts or lead to other inaccuracies using robust test

Re: [gmx-users] #coordinates do not match

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Re: [gmx-users] Long range Lennard Jones

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Re: [gmx-users] Re: Force Field for peptides and proteins

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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical

[gmx-users] g_select help

: one of the values for comparison missing g_select -s DOPC_0.5chl.gro -select 'resname DOPC and resname Cholesterol' works perfectly fine. What is the problem? Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute

Re: [gmx-users] g_select help

Thank you very much. My bilayers were initially built with packmol which is probably why z6 worked. I will keep this in mind. On Wed, Sep 25, 2013 at 9:46 PM, Teemu Murtola teemu.murt...@gmail.comwrote: Hello, On Wed, Sep 25, 2013 at 5:48 PM, rajat desikan rajatdesi...@gmail.com wrote: I

Re: [gmx-users] g_select help

Basic question: How do I verify that the right atoms were chosen in the index file? There are a lot of atoms. On Wed, Sep 25, 2013 at 9:52 PM, rajat desikan rajatdesi...@gmail.comwrote: Thank you very much. My bilayers were initially built with packmol which is probably why z6 worked. I

Re: [gmx-users] g_select problem

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Re: [gmx-users] how to calculate kinetic constant?

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Re: [gmx-users] how to calculate kinetic constant?

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Re: [gmx-users] CHARMM36 force field available for GROMACS

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Re: [gmx-users] CHARMM36 force field available for GROMACS

jalem...@vt.edu wrote: On 10/9/13 7:03 AM, rajat desikan wrote: Superb stuff, Justin. Thank you so much. Is it asking too much for a brief list of the test systems that you used? Thanks again. We tested everything, at least in terms of representative examples. Single amino acids, full

[gmx-users] Continuing runs from 4.5.4 in 4.6.3

for later analysis? I notice that I cannot use a 4.6.3 .cpt and .tpr in 4.5.4. Any input will be appreciated. Thanks. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users

Re: [gmx-users] Continuing runs from 4.5.4 in 4.6.3

Thank you, Mark! On Wed, Oct 23, 2013 at 2:56 PM, Mark Abraham mark.j.abra...@gmail.comwrote: On Oct 23, 2013 7:24 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi, We recently had a software upgrade in our cluster from gromacs 4.5.4. to gromacs 4.6.3.. I need to continue

[gmx-users] Gromos54a8

to gromacs...can you help me here?) Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

Re: [gmx-users] Gromos54a8

Lemkul jalem...@vt.edu wrote: On 10/24/13 6:43 AM, rajat desikan wrote: Dear all, I want to use the Gromos54A8 FF in gromacs. They are available in gromos format in http://www.gromos.net/main.pl ATB is yet to release it in gromacs format. I want to undertake the conversion of this FF

Re: [gmx-users] Gromos54a8

Thanks Justin! If I manage to port it, I will share in the user contributions. Regards, On Thu, Oct 24, 2013 at 6:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 9:00 AM, rajat desikan wrote: Hi Justin, Thanks for the comments. Since the script was written in 2009, I don't want

Re: [gmx-users] Gromos54a8

Thank you so much, Djurre. I will do some tests with protein-membrane systems in mind and share it with the community. I will see if I can reproduce the results in the 54A8 paper. On Fri, Oct 25, 2013 at 1:01 PM, Djurre de Jong-Bruinink djurredej...@yahoo.com wrote: Dear Rajat Desikan, I

[gmx-users] All-bonds vs. H-bonds using CHARMM36

a POPC bilayer. Can someone with experience please shed some light on this? P.S.: Klauda et al., has posted their .mdp for POPE in gromacs on lipidbook. Their .mdp constrains h-bonds http://lipidbook.bioch.ox.ac.uk/uploads/package/CHARMM36/48-POPE-wurl/v1/charmm_npt.mdp Thank you. -- Rajat

Re: [gmx-users] All-bonds vs. H-bonds using CHARMM36

Thank you, Justin! I did intend to use h-bonds for the CHARMM36 simulations and all-bonds elsewhere (depending on the FF). I just wanted some clarity before I proceeded. On Fri, Nov 1, 2013 at 1:49 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/31/13 2:21 PM, rajat desikan wrote: Hi

[gmx-users] CHARMM .mdp settings for GPU

you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

[gmx-users] Re: CHARMM .mdp settings for GPU

Dear All, Any suggestions? Thank you. -- View this message in context: http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] Re: CHARMM .mdp settings for GPU

. I would probably use vdwtype = cut-off, vdw-modifier = potential-shift-verlet and rcoulomb=rlist=rvdw=1.2, but I don't run CHARMM simulations for a living ;-) Mark On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan rajatdesi...@gmail.com wrote: Dear All, Any suggestions? Thank you

[gmx-users] Re: CHARMM .mdp settings for GPU

: Reasonable, but CPU-only is not 100% conforming either; IIRC the CHARMM switch differs from the GROMACS switch (Justin linked a paper here with the CHARMM switch description a month or so back, but I don't have that link to hand). Mark On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan

[gmx-users] Trouble calculating MSD after removing COM for upper and lower leaflets

(resname_DPPC_and_name_P8_and_res_com_z4.3_0.000) has 192 elements There is one group in the index Reading frame 60 time 20600.000 Segmentation fault (core dumped) Any ideas? Is there anything wrong with my workflow? Thanks. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept

Re: [gmx-users] Trouble calculating MSD after removing COM for upper and lower leaflets

you do? Do you see any error in my workflow? Thanks. Appreciate any suggestions... On Sat, Nov 9, 2013 at 7:16 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/9/13 5:24 AM, rajat desikan wrote: Hi All, I have a few older membrane simulations for which the COM for the upper and lower

Re: [gmx-users] Trouble calculating MSD after removing COM for upper and lower leaflets

Hi Justin, Thanks for your time. I think I will use g_traj to spit out the P8 coordinates from upperP8_center_pbcnojump.xtc and write my own little MSD routine :) On Sat, Nov 9, 2013 at 11:36 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/9/13 11:37 AM, rajat desikan wrote: Hi Justin, 1

[gmx-users] Re: CHARMM .mdp settings for GPU

: On 11/7/13 11:32 PM, Rajat Desikan wrote: Dear All, The setting that I mentioned above are from Klauda et al., for a POPE membrane system. They can be found in charmm_npt.mdp in lipidbook (link below) http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html Is there any reason

[gmx-users] Bilayer COM removal issue: Large VCM

suggestions. Thank you. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

[gmx-users] Re: Bilayer COM removal issue: Large VCM

Hi All, Any suggestions? Thanks, On Mon, Nov 11, 2013 at 12:38 AM, rajat desikan rajatdesi...@gmail.comwrote: Hi All, I am experiencing a few problems in membrane simulations wrt COM removal. I downloaded a 400 ns pre-equilibrated Slipid-DMPC membrane with all the accompanying files. I

Re: [gmx-users] Re: Bilayer COM removal issue: Large VCM

by regenerating velocities, or by running short cycles with the time step increasing from very small to normal. Hope it helps, Tsjerk On Wed, Nov 13, 2013 at 8:06 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi All, Any suggestions? Thanks, On Mon, Nov 11, 2013 at 12:38 AM

Re: [gmx-users] Re: Bilayer COM removal issue: Large VCM

lower SOL ; Couple lipid leaflets and SOL separately tau-t= 0.1 0.1 0.1 ; Time constant for temperature coupling ref-t= 310 310 310 ; Desired temperature (K) On Wed, Nov 13, 2013 at 4:07 PM, rajat desikan rajatdesi

Re: [gmx-users] How to construct mixed lipid bilayer

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 -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx