Re: [gmx-users] Running Replica Exchange with Solute Tempering (REST2) with CHARMM36M

Thank you in advance, Aram -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing

Re: [gmx-users] Running Grompp in reverse and backing up MD data

variant that would make this possible, but so far have not managed it. Cheers Paul On 29/11/2018 16:53, Thomas Piggot wrote: You can get an mdp from a tpr using gmx dump -om Cheers Tom On 29/11/2018 14:58, Peter Kroon wrote: Hi all, thanks for all the feedback. @Milan: I've made a tal

Re: [gmx-users] Running Grompp in reverse and backing up MD data

sers&data=01%7C01%7Ct.piggot%40soton.ac.uk%7C03dfb628bcce402f2bb608d6560b4e4e%7C4a5378f929f44d3ebe89669d03ada9d8%7C1&sdata=mWPSzxorWo0e90ORua9pfXlcWttODwLXon5DVA7VkJw%3D&reserved=0 or send a mail to gmx-users-requ...@gromacs.org. -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. --

Re: [gmx-users] Fwd: Adding new atom types

e [ pairtypes ]? And if the parameters are not there they will be calculated by the fudgeLJ. Regards, Alex On Thu, Sep 6, 2018 at 10:58 AM Thomas Piggot wrote: The GROMOS force fields are somewhat different to the others in that they provide specific 1-4 interactions by having several different C1

Re: [gmx-users] Fwd: Adding new atom types

edit the ffnonbonded.itp/[ nonbond_params ] and ffnonbonded.itp/[ pairtypes ] for the interactions of the new atom? or the [ nonbond_params ] and [ pairtypes ] can be descided/governed by normal combination rule used in the FF, so that I do not need to put them in [ nonbond_params ] and ffnonbonded.it

Re: [gmx-users] Dihedrals/Impropers

e checked. The use of impropers depends on the force field and its convention. -Justin -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting

Re: [gmx-users] breaking lipid A tail in minimization

By the way, the link to the paper needs to not include the final bracket: https://www.cell.com/structure/fulltext/S0969-2126(18)30132-1 On 14/06/18 18:40, Thomas Piggot wrote: What you are seeing sounds just like a periodic boundary visualisation issue (http://www.gromacs.org/Documentation

Re: [gmx-users] breaking lipid A tail in minimization

of shahrkord university, Iran -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mail

Re: [gmx-users] Looking for a Gromacs' tool to find lipid molecules which are located in a shell in the x-y plane around a drug molecule intercalated in a bilayer

ailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Ca

Re: [gmx-users] The sign of deuterium order parameter calculated by g_order

) by default. Sorry to bother you with this simple question. But I didn't find any clear answer from mail list or manual. It would be appreciated if you could give your insights or comments. https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2017-July/114678.html -Justin

Re: [gmx-users] Software for PDB input for GROMACS

structure for nucleic acids? I suppose I could do this by hand, but I would very much like to avoid this path if I can. Best Regards, Dan -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org

Re: [gmx-users] Conversion Amber to Gromacs

n/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can

Re: [gmx-users] Gromos54a7 electrostatics interactions ?

ut this will for sure be taken into account whenever needed. I used a shortcut, but it is true that I should try to understand why both forcefields don't give similar results (if it is the case). Thanks for your clear and detailed reply ! -- Dr Thomas Piggot Visiting Fellow University of Sout

Re: [gmx-users] Gromos54a7 electrostatics interactions ?

//www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list

Re: [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings

nlike in the normal sugar/carbohydrate GROMOS force fields). You probably will need to go down the route that I suggested previously and manually make the topology though a combination of building blocks available within the GROMOS force field(s). Cheers Tom On 18/08/17 16:52, Thomas Piggot

Re: [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings

imised geometry file?? thank again for your precious help Emiliano On 2017-08-18 17:26, Thomas Piggot wrote: Hi Emiliano, So I had a spare 5 mins and I found your molecule on the ATB: https://atb.uq.edu.au/molecule.py?molid=223816#panel-md Simulating one of these in water doesn't give me

Re: [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings

your simulation procedures. Cheers Tom On 18/08/17 14:46, Thomas Piggot wrote: You shouldn't use PRODRG, well the default output at least (e.g. see http://pubs.acs.org/doi/abs/10.1021/ci100335w). The ATB is generally pretty good, and although it might not be perfect here (e.g. as you have

Re: [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings

roduce the diffuse scattering in the crystals, I think it is quite important to reproduce all the crystal components in order to have a system that is more similar to the real condition. thank you again Emiliano On 2017-08-18 14:22, Thomas Piggot wrote: Hi Peter, I'd imagine that in

Re: [gmx-users] surfactants simulation topology generation with Automated Topology Builder and lincs warnings

apparent weird behavior. should I have to continue to increase the dt with small increments (i.e. 0.0002ps at each run) or can I just trust to the results I have (angles and bonds distributions) using the dt=0.00183 ps?? could the problem of the lincs warning arise from the generation of the topolog

Re: [gmx-users] Scd or -Scd?

That should have read |Scd| and not [Scd] in the last sentence. On 14/07/17 18:40, Thomas Piggot wrote: As far as I'm aware (and happy to be corrected if someone knows better) it is simply a convention that stems from the fact that the signs of the order parameters were not origi

Re: [gmx-users] Scd or -Scd?

data reported in articles as -S_CD (minus S_CD)? Thanks,Ganj -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

Re: [gmx-users] Replica exchange simulations more than number of processor

ons. Work continues From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Thomas Piggot Sent: 14 April 2017 14:16:26 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Replica exchange simulations more than number of processor Hi Chris, This is interesting. Do you

Re: [gmx-users] Replica exchange simulations more than number of processor

org_gmx-users-boun...@maillist.sys.kth.se < gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Thomas Piggot Sent: 14 April 2017 09:23:35 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Replica exchange simulations more than number of processor In addition, using another te

Re: [gmx-users] Error In Umbrella sampling.

cs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't p

Re: [gmx-users] Replica exchange simulations more than number of processor

romacs.org. -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * Fo

Re: [gmx-users] Order parameter for double bonded lipids

ar 2017 00:36, "Thomas Piggot" wrote: How did you get/make the itp for POPG, this isn't available from the Tieleman group website. The Berger parameters don't work well for PG. For example, you will see ring like structures in the head group if you look at the simulations in s

Re: [gmx-users] Order parameter for double bonded lipids

u know any gromacs tools or other programs that calculatg the area per lipid and bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM but it only works with bilyer lipids. thanks. Merril. On 10 Mar 2017 00:19, "Thomas Piggot" wrote: Sort of. The saturated carbons after the

Re: [gmx-users] Order parameter for double bonded lipids

e the full lipid length but can be used to assess the monolayer behaviour roughly. Merril. On 10 Mar 2017 12:04 a.m., "Thomas Piggot" wrote: The order parameters calculated for all the saturated carbons will be correct but the gmx order program doesn't calculate the order param

Re: [gmx-users] Order parameter for double bonded lipids

ith a double bond in the acyl chain.? can I group all the carbon upto the double bond, therefore ignoring the double bond and the rest of the carbons in the chain to calculate order parameter? Is that a reasonable analysis to measure the order of POPG molecules.? Thanks. -- Dr Thomas Piggot Vis

Re: [gmx-users] E. coli's Inner Membrane Lipid Selection

#x27;ll go to a more complex membrane. Thanks again for your time and help! - Jonathan On Sat, Feb 18, 2017 at 2:34 PM, Thomas Piggot wrote: Hi, For 1), perhaps but it depends upon what you are doing and what you are wanting to look at. Force field choice is (IMHO) likely to be more important (and

Re: [gmx-users] E. coli's Inner Membrane Lipid Selection

m using charmm36 2.) Does my lipid selection make sense? If not, why and what would you use? Thank you for your time!! :-) -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_L

Re: [gmx-users] how to arbitrarily increase the XY size of an existing bilayer system (adding more lipids)

acs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr Thomas

Re: [gmx-users] how to arbitrarily increase the XY size of an existing bilayer system (adding more lipids)

ng compute time when generating the larger systems). Thank you for any advice, Chris. -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * C

Re: [gmx-users] Fwd: LJ cut-offs

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromac

Re: [gmx-users] rlist, rcolumb, and rvdw

/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the arch

Re: [gmx-users] How to use Höltje's cholesterol parameters ?

but I am very curious to know the 'usual' protocol that is followed when people only write "Höltje parameters were used". Another solution would be to use the cholesterol topology file found on ATB (manual validation), frequently used by Pr. Alan E. Mark, but never use

Re: [gmx-users] Order parameters negative value

ative values in an order parameters? -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/S

Re: [gmx-users] Melting temperature for the lipid bilayer

ng_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr Thomas Piggot Visiting Fe

Re: [gmx-users] g_membed failure

seems that this is the case because I am using 5.1.2. How could I resolve this problem? How coould I use g_membed in 5.1.2? Or how I could alternatively insert my protein into a membrane bilayer? Thanks again! 2016-09-14 13:47 GMT+03:00 Thomas Piggot : Hi, In more recent versions of GROM

Re: [gmx-users] g_membed failure

ail to gmx-users-requ...@gromacs.org. -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Ma

Re: [gmx-users] Lipid Head group Orientation

romacs.org. -- Chandan Kumar Choudhury Post Doctoral Fellow Clemson University South Carolina USA -- Dr Thomas Piggot Visiting Fellow University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List befo

Re: [gmx-users] GROMOS Topology files for DSPC

(18:0/18:0 PC). I seek to run these with the GROMOS 53a6 force field. Does anybody have topology (itp) files for this molecule? I checked lipidbook and the previous literature but unfortunately could not locate the necessary files. Thanks,John - -- Dr Thomas Piggot University of South

Re: [gmx-users] non-bond

id force field out there and it is quite old. Better combinations would be AMBER+Slipids or CHARMM36+CGenFF. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] Reliability about Lipid Order Parameters in GROMACS

this issue in many years. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_L

Re: [gmx-users] membrane model

On 6/19/15 11:38 AM, Thomas Piggot wrote: Well, the CHARMM ff is not entirely all-atom: http://pubs.acs.org/doi/abs/10.1021/jp410344g True, people have developed UA force fields from CHARMM's all-atom models. My comment was largely motivated by the fact that the official CHARMM3

Re: [gmx-users] membrane model

ry.ca/tieleman/downloads 3. Will CHARMM-gui a good option for build the this particular system? Not if you want a united-atom model. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_List

Re: [gmx-users] POPE lipid from Tieleman's web site, the box of xy dimension will shrink during the simulation

e "pope.itp" ; Include water topology #include "gromos53a6_lipid.ff/spc.itp" ; System specifications [ system ] 340-Lipid POPE and CNP [ molecules ] ; molecule name nr. POPE 340 SOL 6729 Thanks in advance, Nie Xuechuan Shanghai Institute of Applied Physics, Chines

Re: [gmx-users] Carbohydrate force fields in GROMACS

ing! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr Thomas Piggot University of Southampton, UK. -- Grom

Re: [gmx-users] Build oligosaccharide topology with pdb2gmx

Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Dr Thomas Piggot University of Southampton, UK. -- G

Re: [gmx-users] Semiisotropic pressure coupling

.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr Thomas Piggot University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

Re: [gmx-users] adding hydrogen atoms into a POPC membrane

re posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org (mailto:gmx-users-requ...@gromacs.org). -- Dr Thomas Piggot

Re: [gmx-users] NaCl force field with GROMOS 54A7

teractions with each other. The box size in my simulations range from 15 nm to 30 nm. Thank you for your time, Jason Grosch -- Dr Thomas Piggot University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

Re: [gmx-users] problem with Charmm36 ff

requ...@gromacs.org. -- ******** Esteban Pedrueza Villalmanzo e-mails: esteban.pedru...@uv.es espevi1...@hotmail.com -- Dr Thomas Piggot University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http:/

Re: [gmx-users] Inserting aquaporin-1 in a bilayer with multiple lipids

://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Dr Thomas Piggot University of Southampton, UK. -- Gromacs Users mailing list * Please search the a

Re: [gmx-users] adding ATP parms to AMBER99

incorrect parameters. Thanks for your time. -Stephen -- Stephen N. Floor HHMI Fellow of the Helen Hay Whitney Foundation Doudna Group http://doudna.berkeley.edu -- Dr Thomas Piggot University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.or

Re: [gmx-users] "Justifying" 4fs production runs after 1fs equilibrations?

amespace-nabble.view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> -- View this message in context: http://gromacs.5086.x6.nabble.com/Re-Justifying-4fs-production-runs-after-1fs-e

Re: [gmx-users] Forcefield conversion script for POPC lipids

usly error prone, so if anyone know of a script or a smart approach for this, do tell. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical & Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ -- Dr

Re: [gmx-users] question

tp://mackerell.umaryland.edu/~jalemkul ====== -- Dr Thomas Piggot University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.g

Re: [gmx-users] wall problem

pe would be good for my case? thank you very much. Albert On 01/29/2014 05:27 PM, Justin Lemkul wrote: If you want to use walls, you need to specify wall_atomtype, which (per the error message), you did not. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- Gromac

Re: [gmx-users] About membrane protein

otally away from the bilayer. I think that should be something wrong, but cannot find it. Without seeing your exact commands, neither can anyone else. -Justin -- Dr Thomas Piggot University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www

Re: [gmx-users] errors with charmm36 ?

ul advices. The problem solved now. I some kind of mix the old c36 FF with the new one. I just update it in my system few days ago. thanks again for sugguestions. best Albert -- Dr Thomas Piggot University of Southampton, UK. -- Gromacs Users mailing list * Please search the archiv

Re: [gmx-users] AMBER ff10 with Gromacs

rs or send a mail to gmx-users-requ...@gromacs.org. -- Dr Thomas Piggot University of Southampton, UK. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.o