... well, this URL under ans.2 (http://www.bevanlab.biochem. vt.edu/Pages/Personal/justin/gm) isn't working. 404 Not Found is what I'm repeatedly getting. Please rectify/improve. Thanks and regards!
*Amitabh Jayaswal* *PhD Bioinformatics Scholar* *Banaras Hindu University* *Varanasi, U.P., India | PIN-221005* *+* *City Coordinator* *United Nations* *Rio+22 Power India Program* M: +91 (9868 330088 and 7376 019 155) On Thu, Jul 6, 2017 at 12:21 AM, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: gromacs.org_gmx-users Digest, Vol 158, Issue 165 > (Davide Bonanni) > 2. Charge Mutation (State B) for Ions (Hermann, Johannes) > 3. Number of ions in Anionic lipid system- Charmm-GUI (Nidhin Thomas) > 4. simulation at different temperature (Alex Mathew) > 5. Re: simulation at different temperature (Alex) > 6. Re: simulation at different temperature (Alex Mathew) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 5 Jul 2017 17:09:14 +0200 > From: Davide Bonanni <davide.bona...@unito.it> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 158, Issue > 165 > Message-ID: > <CAL99HEKY+QfSrn-cZDPL8W7azA-HAPqxkOSeRYaE+Go9dGstkQ@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear Hannes, > > Thank you very much for your reply, really appreciated. > > > > > Date: Mon, 26 Jun 2017 12:09:45 +0100 > > From: Hannes Loeffler <hannes.loeff...@stfc.ac.uk> > > To: <gromacs.org_gmx-users@maillist.sys.kth.se> > > Cc: gmx-us...@gromacs.org > > Subject: Re: [gmx-users] Fwd: Relative free energy perturbation > > Message-ID: <20170626120945.75215...@stfc.ac.uk> > > Content-Type: text/plain; charset="US-ASCII" > > > > On Mon, 26 Jun 2017 12:25:19 +0200 > > Davide Bonanni <davide.bona...@unito.it> wrote: > > > > > 1) Can I perform the calculation in a single step with soft core > > > potential enabled? I mean, is it correct to transform directly the > > > hydrogen into a chlorine instead of using 2 topologys and 2 > > > complexes, where in the first step I transform the hydrogen into > > > dummy atom, and in the second I transform the dummy atom into > > > chlorine. > > > > Technically speaking you can perfectly do that but in practice it can > > be much more efficient to directly and linearly transform one atom type > > into another (single topology approach). There is no need for a > > softcore potential in this case. Those would only be activated for > > atoms that either appear or disappear i.e. atoms with zero vdW > > parameters. The input and topology files from FEsetup should be all > > you need. > > > Can I have problems if I keep active the softcore potential whether is not > needed? > > > > > 2) Referring to BevanLab Tutorial 6: Free Energy Calculation ( > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gm > > > x-tutorials/free_energy/index.html), I have to perform every step of > > > molecular dynamics at every Lambda value, is that right? > > > > Yes, you will need to do a simulation for every and each lambda step. > > > > > > > 3) I run a test minimization step (mdp file attached) of my complex > > > at the last "init-lambda-state", 15 in my case. Looking at the .trr > > > output file I can see that the bond between the carbon and the > > > hydrogen which should be trasformed is longer than a normal C-H bond, > > > but the atom is still recognized as hydrogen (picture > > > "http://tinypic.com/r/2wp11dh/9": purple -> init-lambda-state = 0 ; > > > blue -> init-lambda-state = 15). I was wondering if this is what I am > > > supposed to see, so if gromacs is considering the state B of my > > > system where I have chlorine bound to carbon instead hydrogen. > > > > What does "recognized as hydrogen" mean? I suspect that what you are > > referring to is the output of some visualisation program because you > > instructed it to interpret that particular atom to be a hydrogen. > > > > What you need to expect to see is that a C-H bond is transformed into a > > C-Cl bond and accordingly the bond length increases. > > > > Of course, It's like you said. I see the bond length to increase as in the > img "http://tinypic.com/r/2wp11dh/9". > Thank you again. > > Cheers, > > Davide Bonanni > > > ------------------------------ > > Message: 2 > Date: Wed, 5 Jul 2017 18:05:08 +0200 > From: "Hermann, Johannes" <j.herm...@lrz.tu-muenchen.de> > To: gmx-us...@gromacs.org > Subject: [gmx-users] Charge Mutation (State B) for Ions > Message-ID: <1a8a1886-71aa-9162-3db1-cf79b0d2d...@lrz.tum.de> > Content-Type: text/plain; charset=utf-8; format=flowed > > Dear all, > > I am doing a FEC via alchemical transformation. In order to keep the > charge constant I plan to mutate ions at the same time. In particular, I > want to change the charge of MG ions. My question is did I manipulate > the .top .itp and .gro file in the right way: > > In the topology.top file I added: > > #include "topol_MG_Hybrid.itp" > > in the beginning and included in the [molecules] section > > MG_HBRID 26 > > at the place where my hybrid MGs begin in the .gro file. In the .tip > file I defined the new moleculetype and the atom: > > [ moleculetype ] > ; Name nrexcl > MG_HBRID 1 > [ atoms ] > ; nr type resnr residue atom cgnr charge mass > typeB chargeB massB > 1 MG 1 MGX MGHBR 1 2 24.305 > MG 2.30769 24.305 > > In the gro file I changed the (formaly regular) MGs to: > > 8702MGX MGHBR55183 -1.480 0.077 2.991 > > I.e. I changed the residue name to MGX and the atom name to MGHBR. I ran > grompp and it compiles without errors. However, I want to make sure, > that this is consistent with gromacs files and that I will change the > charge in the simulation. > > Thank you very much for your help! > > All the best > Johannes > > > -- > ______________________________________ > *Technische Universit?t M?nchen* > *Johannes Hermann, M.Sc.* > Lehrstuhl f?r Bioverfahrenstechnik > Boltzmannstr. 15 > D-85748 Garching > Tel: +49 8928915730 > Fax: +49 8928915714 > > Email: j.herm...@lrz.tum.de > http://www.biovt.mw.tum.de/ > > > > ------------------------------ > > Message: 3 > Date: Wed, 5 Jul 2017 11:17:32 -0500 > From: Nidhin Thomas <nidhin.thomas0...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Number of ions in Anionic lipid system- > Charmm-GUI > Message-ID: <55d343b4-b971-44ff-a428-e5799e1b4...@gmail.com> > Content-Type: text/plain; charset=us-ascii > > Hi Justin, > > Thanks a lot for the prompt reply. > > I used just 400 POPC lipids to build the lipid bilayer and when I added > 150 mM KCl, it added 49 K+ and 49 Cl- to the system. Do you think these > numbers are correct? Could you please tell me how I can check the correct > number of ions? > > The size of the original system (300 POPC + 100 POPG) was (11.7480468 > 11.7480468 8.98 ) nm. If the size of the system is very small to > accommodate the ions, how can I change the size of the system in charmm-gui > ? Or should I just get the bilayer system and add ions by myself using > gonion command in gromacs? > > Thanks, > > Nidhin Thomas > > >> Dear GROMACS Users, > >> > >> I have created a lipid bilayer system (300 POPC + 100 POPG) using > CHARMM-GUI. > >> I want to include 0.150 M KCl in the system. When I use the option in > charmm-gui, it gives 98K+ ions and -2 Cl ion. But when I calculated the > number of ions using the size of simulation box, I am getting 98 ions. > >> > >> Can anyone tell me what I should do to get the exact number of ions in > the system? > >> > > > > CHARMM-GUI calculates an excluded volume due to the solute (protein, > nucleic > > acid, lipids, etc) so using the total box volume is incorrect when > calculating > > the number of ions in solution. The result you're getting tells you > that your > > box is too small (insufficient solvent volume) to achieve 150 mM KCl. > > > >> Would it be correct if I first neutralize the system using 100 K+ ions > and then add 0.15 M KCl ions (49 K+ and 49 Cl-) in the system? > >> > > > > No, because then your effective concentration is much higher than what > you want. > > > > -Justin > > > ------------------------------ > > Message: 4 > Date: Wed, 5 Jul 2017 23:15:17 +0530 > From: Alex Mathew <alexmathe...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] simulation at different temperature > Message-ID: > <CAAW-8xV3xtfsPqBnczmvAvG413rmJS+Abo-LGOeYZ9GpF3BMOw@mail. > gmail.com> > Content-Type: text/plain; charset="UTF-8" > > Dear gmx users, > > I would like to see the temperature dependence of an ion channel/membrane > protein in lipid bilayer system. My plan is to run a simulation at 300 K to > 340 K by increasing 5 K and observing the permeation of molecules, pore > diameter, sec structure .etc. Are there any techniques available to do > this at a time? Or I have to run the independent simulation for all these? > > > ------------------------------ > > Message: 5 > Date: Wed, 5 Jul 2017 12:31:04 -0600 > From: Alex <nedoma...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] simulation at different temperature > Message-ID: <7c89d0a8-6ac3-fd54-608f-ce2604a90...@gmail.com> > Content-Type: text/plain; charset=utf-8; format=flowed > > Of course: http://manual.gromacs.org/online/mdp_opt.html -- see > 'simulated annealing'. > > Alex > > > On 7/5/2017 11:45 AM, Alex Mathew wrote: > > Dear gmx users, > > > > I would like to see the temperature dependence of an ion channel/membrane > > protein in lipid bilayer system. My plan is to run a simulation at 300 K > to > > 340 K by increasing 5 K and observing the permeation of molecules, pore > > diameter, sec structure .etc. Are there any techniques available to do > > this at a time? Or I have to run the independent simulation for all > these? > > > > ------------------------------ > > Message: 6 > Date: Thu, 6 Jul 2017 00:21:29 +0530 > From: Alex Mathew <alexmathe...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] simulation at different temperature > Message-ID: > <CAAW-8xWpeOiyMjP5wXjd3m1Ado6huFHA4SfzAg79e_iZZk+O1w@mail.gmail. > com> > Content-Type: text/plain; charset="UTF-8" > > Dear Alex, > > I guess this is annealing and which will give only one output.xtc, I'm > looking for full dynamics of the system (say 100 ns for each temperature, > 300 K,305 K....340 K ). Further, I need to compare the results with each > other. > > Thank you. > > > ------------------------------ > > -- > 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 > > * 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. > > End of gromacs.org_gmx-users Digest, Vol 159, Issue 24 > ****************************************************** > -- 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 * 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.