Re: [gmx-users] Charges in vacuum simulation
If in vacuum, I would add hydrogens via covalent bonds. Dr. Vitaly V. Chaban On Mon, Oct 28, 2013 at 10:29 AM, Richa Singh wrote: > Hi all, > > I'm trying to run a vacuum simulation of my protein which has a non-zero > charge. > How to deal with this charge? Can I add counter ions in to my system? > Would it be energetically stable? > > How can one bring a protein to its isoelectric point? > -- > 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)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 -- 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)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
Re: [gmx-users] Charges for calculation of Coulomb interaction
On Thu, Apr 11, 2013 at 5:09 AM, fantasticqhl wrote: > Dear GMX users, > > Just a simple question, are the Coulomb interactions calculated using > charges from ffnonbonded.itp or aminoacid.rtp? > > Normally, they are the same. However, if I modify some charges for some > atoms (for example CB) of some residues in the aminoacid.rtp, > but do not modify in ffnonbonded.itp because some other residues would > still used the old charges, how will gromacs treat the calculations? > Right now I know the best option is introducing new atom types. Thanks > very much! > > Charges from ffnonbonded.itp are never read. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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)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
Re: [gmx-users] Charges for Coulomb potential
Alright, I understand now. Many thanks for this! Antoine Le 29/08/2012 18:57, Mark Abraham a écrit : On 30/08/2012 3:18 AM, Delmotte, Antoine wrote: Many thanks for your quick response, Mark. So epsilon_r is actually different from the actual relative permittivity (which would be like 80 for water), is that right? You can have an atomistic solvent or a continuum solvent, but not both at once. If so, how does one usually chooses this value of epsilon_r? Is the default value of 1 applicable for most cases (like for simulations in water), or should one obtain it from the literature somehow? The force field defines it (normally to 1). Mark Thank you, Antoine On 29/08/12 14:47, Mark Abraham wrote: On 08/29/2012 11:08 PM, Delmotte, Antoine wrote: Dear Gromacs users, I would like to know which charges are used by Gromacs in the calculation of electrostatic interactions in the standard coulomb potential: E_electrostatics = 138.935 * q1 * q2 / (epsilon_r * r_12); Are q1 and q2 the values tabulated in the file "aminoacids.rtp" of the force field used? If you use pdb2gmx to generate your .top, yes. More generally, GROMACS uses the charges found in the .top. Could you also please redirect me towards the relevant literature for the calculation of epsilon_r in Gromacs? (or does Gromacs uses a fixed epsilon_r?) You choose it. See parts of manual 4.1 and 7.3 Mark -- 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)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
Re: [gmx-users] Charges for Coulomb potential
On 30/08/2012 3:18 AM, Delmotte, Antoine wrote: Many thanks for your quick response, Mark. So epsilon_r is actually different from the actual relative permittivity (which would be like 80 for water), is that right? You can have an atomistic solvent or a continuum solvent, but not both at once. If so, how does one usually chooses this value of epsilon_r? Is the default value of 1 applicable for most cases (like for simulations in water), or should one obtain it from the literature somehow? The force field defines it (normally to 1). Mark Thank you, Antoine On 29/08/12 14:47, Mark Abraham wrote: On 08/29/2012 11:08 PM, Delmotte, Antoine wrote: Dear Gromacs users, I would like to know which charges are used by Gromacs in the calculation of electrostatic interactions in the standard coulomb potential: E_electrostatics = 138.935 * q1 * q2 / (epsilon_r * r_12); Are q1 and q2 the values tabulated in the file "aminoacids.rtp" of the force field used? If you use pdb2gmx to generate your .top, yes. More generally, GROMACS uses the charges found in the .top. Could you also please redirect me towards the relevant literature for the calculation of epsilon_r in Gromacs? (or does Gromacs uses a fixed epsilon_r?) You choose it. See parts of manual 4.1 and 7.3 Mark -- 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)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
Re: [gmx-users] Charges for Coulomb potential
Many thanks for your quick response, Mark. So epsilon_r is actually different from the actual relative permittivity (which would be like 80 for water), is that right? If so, how does one usually chooses this value of epsilon_r? Is the default value of 1 applicable for most cases (like for simulations in water), or should one obtain it from the literature somehow? Thank you, Antoine On 29/08/12 14:47, Mark Abraham wrote: On 08/29/2012 11:08 PM, Delmotte, Antoine wrote: Dear Gromacs users, I would like to know which charges are used by Gromacs in the calculation of electrostatic interactions in the standard coulomb potential: E_electrostatics = 138.935 * q1 * q2 / (epsilon_r * r_12); Are q1 and q2 the values tabulated in the file "aminoacids.rtp" of the force field used? If you use pdb2gmx to generate your .top, yes. More generally, GROMACS uses the charges found in the .top. Could you also please redirect me towards the relevant literature for the calculation of epsilon_r in Gromacs? (or does Gromacs uses a fixed epsilon_r?) You choose it. See parts of manual 4.1 and 7.3 Mark -- 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)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
Re: [gmx-users] Charges for Coulomb potential
On 08/29/2012 11:08 PM, Delmotte, Antoine wrote: Dear Gromacs users, I would like to know which charges are used by Gromacs in the calculation of electrostatic interactions in the standard coulomb potential: E_electrostatics = 138.935 * q1 * q2 / (epsilon_r * r_12); Are q1 and q2 the values tabulated in the file "aminoacids.rtp" of the force field used? If you use pdb2gmx to generate your .top, yes. More generally, GROMACS uses the charges found in the .top. Could you also please redirect me towards the relevant literature for the calculation of epsilon_r in Gromacs? (or does Gromacs uses a fixed epsilon_r?) You choose it. See parts of manual 4.1 and 7.3 Mark -- 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)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
Re: [gmx-users] charges
On 2012-04-02 20:40, R.Perez Garcia wrote: Dear prof. van der Spoel, I know.. Dr. Alex de Vries is supervising me for my colloquium. Unfortunately (for me), they are very busy and (mainly) I am doing four months stage at Perugia universityv (It) which means I can not personally ask...so I prefer to ask the list. Thank you for your answer, even if the literature concerning virtual charges is not a lot, I will keep looking. Best regards: R It's in the manual. [ virtual_sites2 ] ; k i j type constant 3 1 2 1 0.5 will give you a virtual site 3 half-way atoms 1 & 2. On 02-04-12, *David van der Spoel * wrote: On 2012-04-02 20:29, R.Perez Garcia wrote: >Dear GROMACS users, >I would like to place the charge more localized in the "bonds region" >and not exactly in the atoms. >Please let me know if you know there is a way to do this in GROMACS. >Thank you in advance, R > > Yes, using virtual sites. There's an expert group of gromacs users at the department of biophysical chemistry at your university, Marrink. You may want to talk to then. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se -- 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)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 -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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)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
Re: [gmx-users] charges
Dear prof. van der Spoel, I know.. Dr. Alex de Vries is supervising me for my colloquium. Unfortunately (for me), they are very busy and (mainly) I am doing four months stage at Perugia universityv (It) which means I can not personally ask...so I prefer to ask the list. Thank you for your answer, even if the literature concerning virtual charges is not a lot, I will keep looking. Best regards: R On 02-04-12, David van der Spoel wrote: > On 2012-04-02 20:29, R.Perez Garcia wrote: > >Dear GROMACS users, > >I would like to place the charge more localized in the "bonds region" > >and not exactly in the atoms. > >Please let me know if you know there is a way to do this in GROMACS. > >Thank you in advance, R > > > > > Yes, using virtual sites. > There's an expert group of gromacs users at the department of biophysical > chemistry at your university, Marrink. You may want to talk to then. > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > -- > gmx-users mailing list gmx-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)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 > > -- 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)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
Re: [gmx-users] charges
On 2012-04-02 20:29, R.Perez Garcia wrote: Dear GROMACS users, I would like to place the charge more localized in the "bonds region" and not exactly in the atoms. Please let me know if you know there is a way to do this in GROMACS. Thank you in advance, R Yes, using virtual sites. There's an expert group of gromacs users at the department of biophysical chemistry at your university, Marrink. You may want to talk to then. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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)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
Re: [gmx-users] Charges
Tanos Franca wrote: Dear gmx users, Does someone know in which file GROMACS store the information on the protein charge. I've seen that after running pdb2gmx or grompp the system charge is shown in the screen but we would like to know if this information is recorded in some file. It's in your topology. The "qtot" entry keeps a running total of the charge on the protein. The last line in [atoms] indicates the overall net charge. -Justin With my best regards, Tanos C. C. Franca. Coordinator of the Graduate Program in Chemistry. Military Institute of Engineering Rio de Janeiro - RJ Brazil. -- 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 -- 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)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
Re: [gmx-users] Charges?
Triguero, Luciano O wrote: Hi gromacs guru! Does any know a clever way on how to convert QM charges to group charges as in shown in the residue topology file? Nope. You should read the documentation for the force field - probably the original published manuscript - and see how the others were developed, and try to do something consistent. There's no reason to expect a correlation between charges calculated with an arbitrary QM method and the partial charge *optimized parameters* used in an arbitrary MM force field. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] charges for non-natural residues with gromos 53a6
Carsten Baldauf wrote:
dear all//
i need to parameterize a non-natural amino acid residue.
i have a problem with assigning the charges, how should i scale them? i
can obtain quantum chemical charges from AM1 to {HF,DFT}/6-31G* and
further, but how to include (scaling, i now where to write them) them in
the force field?
Have you read the original literature that describes the development of
this force field? You should be doing something consistent with that.
Mark
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Re: [gmx-users] charges in polymer
Dmitriy Golubobsky wrote: Dear Guru, i need an advice. i create 3 resudues for my polymer. ( begin-monomer, middle-monomer, end-monomer) optimize geometry and charges in gaussin 6-31G. formalize topology for OPLS force-field. but, i've got a question have i to do RESP of the charges of my monomers according to ff or not? if yes, what have i to use for it. If you are extending a force field, read how they developed that force field and do something consistent. The above looks more like you are making something up entirely, in which case do whatever you like, but you've got a better chance of getting past referees if you either use something close to an existing methodology or demonstrate its effectiveness by comparison with existing simulations or experiments. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
