Re: [gmx-users] Calculating diffusion coefficient in three dimension

@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. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can&#

Re: [gmx-users] strange lincs warning with version 4.6

acs.org/** Support/Mailing_Lists/Search<http://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/M

Re: [gmx-users] which version it is

-- Message: 3 Date: Mon, 19 Nov 2012 16:28:28 + From: Thomas Piggot Subject: Re: [gmx-users] which version it is To: Discussion list for GROMACS users Message-ID: <50aa5e2c.4000...@soton.ac.uk> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Hi, As I under

Re: [gmx-users] which version it is

11/19/12 11:28 AM, Thomas Piggot wrote: Hi, As I understand it, the current and most up to date CHARMM protein force field (as included in both the charmm27 and charmm36 force field directories) is the CHARMM22 protein force field with the CMAP correction. In other words there would be no

Re: [gmx-users] which version it is

71.65 kB15:42, 25 Sep 2012TomPiggot I am just wondering, is the the one with CHARMM27_protein+Charmm36_lipids or it is CHARMM36_protein+CHARMM36_lipids? thank you very much best Albert -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromac

Re: [gmx-users] Problem with equilibrated lipid bilayer structure

(instead of just bonds to hydrogen atoms) with this force field. We found that we needed to increase the accuracy of the LINCS settings when constraining all bonds to ensure energy conservation. Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing list

Re: [gmx-users] Problem with equilibrated lipid bilayer structure

ribe 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 -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/m

Re: [gmx-users] Coordinate file for lipid bilayer

ww interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users *

[gmx-users] Reference for CHARMM36 Force Field Conversion

the conversion for DPPC and POPC membrane systems (in terms of single point energies calculated in both GROMACS and NAMD) is provided in the supporting information of this work. Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer

t does not seem the mdp file I used is able to get more common APL and diffusion values even when averaging over a large number of simulations. As for the pressure in the x/y direction, is it more appropriate to use 1 atm or 0 atm for bilayer simulations? -David -- Dr Thomas Piggot University

Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer

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 -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailma

Re: [gmx-users] Smaller Area Per Lipid for DPPC Bilayer

ial forces dictate the velocities. I suppose if the run is stable enough, this is not a huge problem, but in general this combination is not recommended. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailma

[gmx-users] ParmBSC0 Force Field Contribution

: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study Andrew T. Guy, Thomas J. Piggot, and Syma Khalid Biophysical Journal Volume 103, Issue 5, 5 September 2012, Pages 1028–1036 http://dx.doi.org/10.1016/j.bpj.2012.08.012 Cheers Tom -- Dr Thomas Piggot

Re: [gmx-users] When to use Dispersion Correction for Lipid Bilayers

earch 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 -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing list

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

erface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text mes

Re: [gmx-users] CHARMM36 - Smaller Area per lipid for POPE - Why?

/lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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. Use the www interface or send it to gmx-use

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

ld. Rather using combination rules (as for example done in the Berger/OPLS combination) is probably better. Cheers Tom On 19/07/12 00:15, Justin Lemkul wrote: On 7/18/12 6:57 PM, Thomas Piggot wrote: Hi, Justin, I am interested by your comments regarding the CHARMM lipids. In particul

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

s. 54A7 is certainly better in terms of helical stabilization, from what I can see. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allow

Re: [gmx-users] Berger lipid

se the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users *

Re: [gmx-users] Trajectories

.bmc.uu.se <mailto:er...@xray.bmc.uu.se> http://www2.icm.uu.se/molbio/elflab/index.html -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gro

Re: [gmx-users] Re: dangling bond at at one of the terminal ends

you need to have all the atoms present and named as the force field expects them to be. You can't have anything missing or anything extra. Also, copying and pasting error messages directly from the terminal is vastly more helpful than a description. -Justin -- Dr Thomas Piggot Universit

[gmx-users] Lipid A Topology

group website (http://www.personal.soton.ac.uk/sk2x07/index.php), along with a structure file for this molecule. Cheers Tom Piggot -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search

Re: [gmx-users] forcefields for lipids

o you suggest this forcefield for this kind of bilayer too? Thanks so much for your reply. Sincerely, Shima *From:* Thomas Piggot *To:* Discussion list for GROMACS users *Sent:* Tuesday, May 22, 2012 10:15 PM *Subject:* Re: [gmx-

Re: [gmx-users] forcefields for lipids

*From:* Thomas Piggot *To:* Discussion list for GROMACS users *Sent:* Tuesday, May 22, 2012 7:39 PM *Subject:* Re: [gmx-users] forcefields for lipids Thanks Joakim, I will be very interested to see how these different lipids behave. This looks like it could be a really useful force field. We

Re: [gmx-users] forcefields for lipids

:48 +0100 From: Thomas Piggot Subject: Re: [gmx-users] forcefields for lipids To: Discussion list for GROMACS users Message-ID: <4fbb8b6c.70...@soton.ac.uk> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Hi Joakim, I am interested to know what other lipids this forc

Re: [gmx-users] forcefields for lipids

submitted, but for now have a look at this published paper: J. Phys. Chem. B, 2012, 116 (10), 3164-3179, doi: 10.1021/jp212503e All our parameters are available at on Lipidbook. Let me know if you need anything else! Best, J -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users

Re: [gmx-users] forcefields for lipids

.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- 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&

Re: [gmx-users] Best Force Field for a Membrane Protein

s-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org htt

Re: [gmx-users] Ion parameters in OPLS AA force field

Jorgensen et al. from 2001. However I was not able to find the corresponding atom types in this article and so far also not in any other article of the OPLS-AA authors. Does anyone have an idea where these parameters come from ? /Flo -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users

Re: [gmx-users] Literature reading on DispCorr for energy and pressure

complished, and what approximations it introduces and assumptions it makes. Section 4.8 of the manual gives many details, but I am curious if you can recommend any review-type articles about this correction. Thank you very much for your time! Andrew DeYoung Carnegie Mellon University -- D

Re: [gmx-users] forcefield.itp file for gromos45a3 and oplsaa

't find. Mark -- Dr Thomas Piggot University of Southampton, UK. -- 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 (

Re: [gmx-users] Parametrisation of the heteroatomic pdb

n and compare with mdrun -rerun Rconfiguration.gro -s Lconfiguration. -- Dr Thomas Piggot University of Southampton, UK. -- 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/Mai

Re: [gmx-users] source of opls Mg2+ parameters?

eters that are distributed with gromacs and verified that these c6/c12 values do not match the sigma/epsilon opls values after a conversion with g_sigeps. Thank you very much for your time and assistance, Chris. -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing lis

Re: [gmx-users] Charmm27 ff for membrane protein simulation

the force field is necessary. Run pdb2gmx on a single lipid molecule, convert the .top to .itp (see the wiki) and #include it in the .top for your protein, just like in my tutorial. -Justin Thank you for help James -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing li

Re: [gmx-users] topologies for POPE and DMPE

bilayer. Do, you have POPC structure and itp files parameterised by CHARMM 27 FF. Regards, Pramod On Mon, Oct 17, 2011 at 12:07 PM, Thomas Piggot wrote: Hi Roy, PE lipids are less frequently used than PC ones and there are fewer topologies available. Also it has been shown that using the Berger

Re: [gmx-users] topologies for POPE and DMPE

POPE and DMPE. Anybody knows where can i get the topologies file for POPE and DMPE ? Any help is much appreciated. Thanks a lot! Roy -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinf

Re: [gmx-users] CHARMM 36 force field

the NPT ensemble, may I have access to it? Best regards Giovanni -- Dr Thomas Piggot University of Southampton, UK. -- 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

Re: [gmx-users] CHARMM36 force field

? Best regards Giovanni -- Dr Thomas Piggot University of Southampton, UK. -- 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 pos

Re: [gmx-users] MARTINI / all-atom mapping

http://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 <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailin

Re: [gmx-users] Error from residues added to rtp file

the origin of this error, and on what I can do to correct it. I am using Gromacs 4.5.3. Thanks a lot in advance, Antoine -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] Charge groups in Charmm for lipids

. Sorry for any problems caused by this. Cheers Tom On 06/08/11 02:28, Thomas Piggot wrote: Sure, I will upload a GROMACS 4.5.4 version of the force field files to the website. Cheers Tom On 06/08/11 01:34, Peter C. Lai wrote: On 2011-08-05 06:48:09PM -0500, Thomas Piggot wrote: Hi, Yes, this

Re: [gmx-users] Charge groups in Charmm for lipids

Sure, I will upload a GROMACS 4.5.4 version of the force field files to the website. Cheers Tom On 06/08/11 01:34, Peter C. Lai wrote: On 2011-08-05 06:48:09PM -0500, Thomas Piggot wrote: Hi, Yes, this was done on purpose to reflect the different use of charge groups in CHARMM and GROMACS

Re: [gmx-users] Charge groups in Charmm for lipids

arge. Was this changed on purpose? The beta version seems correct to me, but am I missing something as to why this change would be made? Thanks -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

issue regarding this on redmine. Cheers Tom Thomas Piggot wrote: Hi, Both the trajectories are 100 ns in length (plus I have a repeat of each simulation using different starting velocities). The results from a block analysis, and analysis of the repeat simulations, give almost identical

Re: [gmx-users] All-atom topologies for lipid head groups

alike. If you really want an AA representation of your molecules, you're probably better off just applying the CHARMM force field to the whole system. The latest version of Gromacs supports CHARMM, which includes a number of common lipids. -Justin -- Dr Thomas Piggot University of Sou

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

ng to calculate the order parameters from the all-atom CHARMM36 simulations using a different bit of code, I will report back with the results if we can get this to work. Cheers Tom Justin A. Lemkul wrote: Thomas Piggot wrote: Hi Igor, Thanks for the reply but I think you slightly missed the point

Re: [gmx-users] Calculation of unsaturated deuterium order parameters for POPC

ollowing values 0.0738068 -0.000533683 that you should then replace in the correct positions in the sn2 output good luck, and sorry if i'm missing the point :| igor Igor Marques On Wed, Jun 8, 2011 at 5:53 PM, Thomas Piggot <mailto:t.pig

[gmx-users] Calculation of unsaturated deuterium order parameters for POPC

an give Cheers Tom -- Dr Thomas Piggot University of Southampton, UK. -- 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)s

Re: AW: Re: [gmx-users] where can I download POPC membrane file?

posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org > <mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/

Re: [gmx-users] lipids per area charmm36 popc

ly enough to make solid conclusions about membranes. Lipid rotational relaxation is on the order of 5 ns, and translational relaxation about 10 ns. I'd say you need at least 20 ns of simulation to make any real conclusions, with some of that of course discarded as equilibration. -Jus

Re: [gmx-users] How to use Inflategro with different lipid types

pid headgroups in the z-dimension only during this procedure so the lipids do not simply slam into one another and distort the membrane. Once you've achieved a reasonable membrane, solvate and equilibrate for a longer period of time in the presence of solvent and absence of any restraints.

Re: [gmx-users] help on converting charmm/cgenff parameters to gromacs

. If one were to use some other tool for generating topologies, I don't know whether charges missing from a [moleculetype] definition are looked up in ffnonbonded.itp. Mark -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists

Re: [gmx-users] Re: change in the secondary structure after simulation

- -- ==== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

Re: [gmx-users] grompp charge group radii larger than rlist

e... Any idea as to what causes this problem? Much obliged for your help. Cheers, Ramon -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.grom

Re: [gmx-users] N-acetyl-d-glucosamine parameters

appreciated, Thanks Renato -- Dr Thomas Piggot University of Southampton, UK. -- 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] galactose bond stretch

I have added an issue on redmine. Cheers Tom Justin A. Lemkul wrote: Thomas Piggot wrote: Whilst this 'problem' you are seeing is probably as Justin has described (a periodic boundary visualisation effect), you should also beware when performing carbohydrate/sugar simulation

Re: [gmx-users] galactose bond stretch

Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- 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 po

Re: [gmx-users] Re:Re: Which FF could be used for protein-RNA MD simulation in GROMACS?

b/site had them. The same is true for lipid and carbohydrate .itp/.rtp libraries. Stephan Watkins -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.g

Re: [gmx-users] CMAP error

the www interface or send it to gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://

Re: [gmx-users] dna, lipid simulation

h University, | Victoria 3800 | Australia | | Tel: +61 3 9902 9376 | Fax: +61 3 9902 9500 | E-mail: itamar.k...@monash.edu <mailto:itamar.k...@monash.edu> ======== -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-use

[gmx-users] Fwd: lateral diffusion coefficients on a spherical surface

Hi, I am forwarding on a message on behalf of one of my colleagues who is having problems sending messages to the list. Please take a look his message and see if you can help him with his problem. Thank you Tom Piggot Original Message Subject:lateral diffusion coef

Re: [gmx-users] Re: gmx-users Digest, Vol 79, Issue 167

kJ/mol) > > USE_CHARGE_GROUP_AND_GMX_4.5.3 AND CHARMM parameters settings > > Energy Average Err.Est. RMSD Tot-Drift > ----------- > Potential

Re: [gmx-users] Discrepancy between -chargegrp and -nochargegrp in simulations with CHARMM ff, Why ?

-568520 24770.264 -165.498 (kJ/mol) Total Energy-463287 24955.755 -165.768 (kJ/mol) I am particularly eager to obtain from you some comments and advices about these findings. Thanks you so much for your help. SA -- Dr Thomas Piggot University of Southampt

Re: [gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2

g_density using only the last frame. > > * Fixed several issues with cmake > > * Several minor fixes. > > > > > > Once again big thanks to all developers for their hard work, and to all users for their contributions! > > > > Happy simulating! > > Rossen >

[gmx-users] Single atom charge group implementation for CHARMM27 in 4.5.2

ssues with cmake * Several minor fixes. Once again big thanks to all developers for their hard work, and to all users for their contributions! Happy simulating! Rossen -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromac

[gmx-users] Re: Charmm36 FF and membrane

small (by XY dimension) for my purpose. I am still trying with Charmm36 FF. Regards On Mon, Nov 1, 2010 at 4:21 PM, Thomas Piggot <mailto:t.pig...@soton.ac.uk>> wrote: Hi, This is more of a GROMACS problem than a specific problem related to this lipid conversion so it i

[gmx-users] Re: Charmm36 FF and membrane

hes. I do not know where I went wrong. Please enlighten me. Best regards. -- Dr. Tusar Bandyopadhyay Theoretical Chemistry Section, Chemistry Group BARC, Trombay Mumbai 400 085 INDIA Tel: 022-2559 0300 email: tusaratb...@gmail.com <mailto:tusaratb...@gmail.com> -- Dr Thomas Piggot University

Re: [gmx-users] New release: 4.5.2

Happy simulating! Rossen -- Dr Thomas Piggot University of Southampton, UK. -- 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'

Re: [gmx-users] who has the force field file of gromos45a4

http://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 -- Dr Thomas Piggot University of Southamp

Re: [gmx-users] Gromos 45A4

t/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- 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)subsc

Re: [gmx-users] CHARMM36 lipid bilayers

st you try running with the CHARMM TIP3P water (tips3p.itp) and see if you get values which are closer to the ones published in the paper you mention. This will be discussed in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär

Re: [gmx-users] CHARMM36 lipid bilayers

see if you get values which are closer to the ones published in the paper you mention. This will be discussed in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field

Re: [gmx-users] CHARMM36 lipid bilayers

in a paper which we hope to have published fairly soon. Cheers Tom Sven Jakobtorweihen wrote: Dear gmx-users, recently Pär Bjelkmar and Thomas Piggot have generated force field files for Charmm36 lipids. I run some simulations to find the best run parameters and to check if the results of the

Re: [gmx-users] How to incorporate WALP and KALP peptide in a Martini bilayer

I ran multiple configurations but in some cases it goes other side of membrane. in some cases, it remained parallel in interface.but never got inserted in a trans-membrane manner. -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] CHARMM36 Force Field

conversion by Par Bjelkmar without any differences seen and allow the simulation of membrane protein systems. If anyone has any questions (or thinks they have found any mistakes!) then feel free to contact me (which is probably best done through the mailing list). Cheers Tom Piggot -- Dr Thomas

Re: [gmx-users] charmm c36 lipids

m everything is the same and report back to the list. I don't see anything which would not work for your script as there are not any major changes to the forcefield in CHARMM36. -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists

Re: [gmx-users] cholesterol

omacs.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 -- Dr Thomas Piggot University of Southampton, UK.

Re: [gmx-users] charmm c36 lipids

would greatly appreciate if you could please send it to me. I am trying to use the new CHARMM36 lipids for a simulation with a membrane protein. Thank-you. Drew Bennett -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.grom

Re: [gmx-users] Issue with Atom Types/Charges/Mass when including ATP in gromos53.a6

ort/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 -- Dr Thomas Piggot University of Southampton, UK. -- gmx

Re: [gmx-users] Problem with pdb2gmx and a new residue

/Support/Mailing_Lists -- Postdoctoral Research Scholar, Department of Chemistry, University of Nevada, Reno. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemku

Re: [gmx-users] ARG Charmm gmx 4.5.1

ce or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive a

Re: [gmx-users] Nucleotides for charmm port

"stream" file and have no idea how to convert it. It should be possible (for someone smarter than me). cheers Dave -- Dr Thomas Piggot University of Southampton, UK. [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type o

Re: [gmx-users] Checkpoint files not being written

ed around a bit in the mdrun code, but I easily lose my place trying to trace what's going on. I've tried specifically adding -cpnum to my mdrun command line, but still I am not receiving any intermediate checkpoint files at the requested -cpt interval. -Justin -- Dr Thomas Piggot Un

Re: [gmx-users] deletion of some water molecules

environment of pr-dna complex and not water molecules being in edges or rest of box. Is there any way to do that? -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

Re: [gmx-users] OPLS-AA topologies for ATP

mber over Charmm? Is it more "compatible" with OPLS? Thanks, Bin On Jun 23, 2010, at 2:48 AM, Thomas Piggot wrote: Well I would suggest you should do some very careful testing to validate the combination of CHARMM charges and one dihedral with the rest of the parameters from OPLS. It is

Re: [gmx-users] OPLS-AA topologies for ATP

e have OPLS-AA topologies for ATP? Thanks, Efrat -- gmx-users mailing listgmx-users@gromacs.org <mailto:gmx-users@gromacs.org> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un

Re: [gmx-users] CG (MARTINI) parameters for RNA

MARTINI force field? All the best, Itamar -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subs

Re: [gmx-users] g_bundle issue

1904 1913 1922 1940 1948 1956 1965 1974 1983 1991 [ bottom ] 2000 2008 2014 2024 2032 2041 2050 2067 2079 2092 2101 2109 2118 2124 2132 2138 2146 Regards, Anirban -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/m

Re: [gmx-users] PMF of ligand transport

org/mailing_lists/users.php -- Aswathy -- Aswathy -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posti

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

pull_geometry=distance to get the complete PMF? Tom Jochen Hub wrote: Thomas Piggot wrote: Jochen thanks for your help. That was what I was afraid of you saying. Oh well, at least this will hopefully provide a useful reference so somebody doesn't make this same mistake. On a side note I noti

Re: [gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

auto off, but I assumed that using -min and -max the -noauto option would have been the 'correct' way to do this. Cheers Tom Jochen Hub wrote: Thomas Piggot wrote: Hi, I am trying to construct a PMF profile for a phosphate ion passing through a membrane protein using umbrell

[gmx-users] PMF profile using g_wham with pull_geometry = distance for ion channel

also tried using g_wham 4.0.7 but with exactly the same issues ,as well as using the pullf.xvg files as input to g_wham. I apologise if I am missing something obvious (or doing something silly!) but any help would be greatly appreciated. Cheers Tom -- Dr Thomas Piggot University of Southampto

Re: [gmx-users] parametrization of FAD

I should also say that there are parameters for FADH(-) available for use with the amber forcefields: http://www.pharmacy.manchester.ac.uk/bryce/amber#cof Tom Thomas Piggot wrote: FAD has been prameterised previously. IIRC the parameters are in the appendix of the thesis of Anton Feenstra

Re: [gmx-users] parametrization of FAD

time (read: weeks or months) to just deriving suitable parameters. The piecemeal approach I describe for FAD seems to work pretty well, but may not always be possible or feasible. http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin Regards, Giulia Gonnelli -- Dr Thomas

[gmx-users] Re: AMBER force fields for ATP

e for the radius and epsilon values, or how to parametrize the P-OS-P bond. I was wondering, if you don't mind, could you point me in the right direction? Thanks very much, Alice Chang Liao Research Group Columbia University -- Thomas Piggot University of Bristol, UK. -- gmx-users

Re: [gmx-users] Software inconsistency error: Not enough water

- > > > > Express yourself instantly with MSN Messenger! MSN Messenger > > > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > > > > > > > -- > > > > gmx-users mailing list gmx-users@gromac

Re: [gmx-users] Software inconsistency error: Not enough water

.gromacs.org/mailing_lists/users.php > > > > > > > > > > Express yourself instantly with MSN Messenger! MSN Messenger > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/

Re: [gmx-users] ATP for

rcsb (http://www.pdb.org/pdb/explore/explore.do?structureId=1QHH) shows ATP with hydrogen. -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Feb 8, 2010 at 8:34 PM, Thomas Piggot <mailto:t.pig...@bristol.ac.uk>> wrote: Are you sure you added it up correctly? I get a nu

Re: [gmx-users] ATP for

values etc. values. Where to get these values Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot mailto:t.pig...@bristol.ac.uk>> wrote: Not sure about amb2gmx.p

Re: [gmx-users] ATP for

-- Chandan kumar Choudhury NCL, Pune INDIA -- Thomas Piggot University of Bristol, UK. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subsc

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