[gmx-users] Fwd: solvent evaporation modeling
Dear André, Thank you for your response. Could you send me such a script? Best -- *** Sako On Mon, Dec 2, 2019 at 12:54 AM SAKO MIRZAIE wrote: > Dear André, > > Thank you for your response. > Could you send me such a script? > > On Sun, Dec 1, 2019 at 7:15 PM André Farias de Moura > wrote: > >> Dear Sako, >> >> we did something like that a few years ago, please take a look at DOI >> 10.1039/C4CP03519D >> for details. >> >> in a nutshell: you need a script that runs a sequence of short >> equilibration and production runs after a number of solvent molecules are >> removed (implying that topology needs to be updated for the number of >> solvent molecules at each round, so the script needs to include some >> parsing of the files as well). >> >> Andre >> >> On Sun, Dec 1, 2019 at 8:03 PM SAKO MIRZAIE >> wrote: >> >>> Hi All, >>> >>> I want to simulate a polymer: protein system in a way that water solvent >>> will evaporated gradually. How should I do that? What parameters are >>> needed >>> to be included in the mdp file. >>> >>> Best >>> >>> >>> >>> -- >>> *** >>> Sako >>> -- >>> 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. >>> >> >> >> -- >> _ >> >> Prof. Dr. André Farias de Moura >> Department of Chemistry >> Federal University of São Carlos >> São Carlos - Brazil >> phone: +55-16-3351-8090 >> > > > -- > *** > Sako > > > > > -- 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.
Re: [gmx-users] solvent evaporation modeling
Dear André, Thank you for your response. Could you send me such a script? On Sun, Dec 1, 2019 at 7:15 PM André Farias de Moura wrote: > Dear Sako, > > we did something like that a few years ago, please take a look at DOI > 10.1039/C4CP03519D > for details. > > in a nutshell: you need a script that runs a sequence of short > equilibration and production runs after a number of solvent molecules are > removed (implying that topology needs to be updated for the number of > solvent molecules at each round, so the script needs to include some > parsing of the files as well). > > Andre > > On Sun, Dec 1, 2019 at 8:03 PM SAKO MIRZAIE > wrote: > >> Hi All, >> >> I want to simulate a polymer: protein system in a way that water solvent >> will evaporated gradually. How should I do that? What parameters are >> needed >> to be included in the mdp file. >> >> Best >> >> >> >> -- >> *** >> Sako >> -- >> 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. >> > > > -- > _ > > Prof. Dr. André Farias de Moura > Department of Chemistry > Federal University of São Carlos > São Carlos - Brazil > phone: +55-16-3351-8090 > -- *** Sako Mirzaie Sako Mirzaie Ph.D. in biochemistry, Assistant Professor, Science Faculty, Islamic Azad University of Sanandaj, Sanandaj, Iran Visiting Professor, Advanced Pharmaceutics & Drug Delivery Laboratory Leslie Dan Faculty of Pharmacy University of Toronto 144 College Street, Toronto, Ontario Canada M5S 3M2 http://scholar.google.com/citations?user=viwZvVAJ=en http://www.scopus.com/authid/detail.url?authorId=54886431500 http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie https://www.researchgate.net/profile/Sako_Mirzaie/publications/ -- 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.
Re: [gmx-users] solvent evaporation modeling
Dear Sako, we did something like that a few years ago, please take a look at DOI 10.1039/C4CP03519D for details. in a nutshell: you need a script that runs a sequence of short equilibration and production runs after a number of solvent molecules are removed (implying that topology needs to be updated for the number of solvent molecules at each round, so the script needs to include some parsing of the files as well). Andre On Sun, Dec 1, 2019 at 8:03 PM SAKO MIRZAIE wrote: > Hi All, > > I want to simulate a polymer: protein system in a way that water solvent > will evaporated gradually. How should I do that? What parameters are needed > to be included in the mdp file. > > Best > > > > -- > *** > Sako > -- > 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. > -- _ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- 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.
[gmx-users] solvent evaporation modeling
Hi All, I want to simulate a polymer: protein system in a way that water solvent will evaporated gradually. How should I do that? What parameters are needed to be included in the mdp file. Best -- *** Sako -- 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.
Re: [gmx-users] Charmm27 and Charmm36 atomtypes assignments for polymer
Dear Justin, Thank you very much for your response. I copied the ITP file that generated Charmm-gui. I am sorry for copied this long residue topology. The residue contains two capping groups that belong to first six atoms and the last six atoms. I thought that if I cut the first 6 atoms, the rest is the last residue. Similarly, after cut the last 6 atoms, the rest will show the first residue of the polymer. If I cut both ends, I can get the internal residue of the polymer. However, the first and the last 6 atoms possess + 0.002 net charges. Because of this difference, my three residues assigned as the non-neutral from pdb2gmx. How can I solve this problem without any QM calculations? [ atoms ] ; nr type resnr residu atom cgnr charge mass 1 NG321 1 PEI N1 1 -0.87614.0070 ; qtot -0.876 2 HGPAM2 1 PEI H1 2 0.298 1.0080 ; qtot -0.578 3 HGPAM2 1 PEI H2 3 0.298 1.0080 ; qtot -0.280 4 CG321 1 PEI C1 4 0.10212.0110 ; qtot -0.178 5 HGA2 1 PEI H3 5 0.090 1.0080 ; qtot -0.088 6 HGA2 1 PEI H4 6 0.090 1.0080 ; qtot 0.002 7 CG321 1 PEI C2 7 0.09112.0110 ; qtot 0.093 8 HGA2 1 PEI H5 8 0.090 1.0080 ; qtot 0.183 9 HGA2 1 PEI H6 9 0.090 1.0080 ; qtot 0.273 10 NG301 1 PEI N2 10 -0.81914.0070 ; qtot -0.546 11 CG321 1 PEI C3 11 0.09112.0110 ; qtot -0.455 12 HGA2 1 PEI H7 12 0.090 1.0080 ; qtot -0.365 13 HGA2 1 PEI H8 13 0.090 1.0080 ; qtot -0.275 14 CG321 1 PEI C4 14 0.00512.0110 ; qtot -0.270 15 HGA2 1 PEI H9 15 0.090 1.0080 ; qtot -0.180 16 HGA2 1 PEIH10 16 0.090 1.0080 ; qtot -0.090 17 NG311 1 PEI N3 17 -0.66614.0070 ; qtot -0.756 18 HGPAM1 1 PEIH11 18 0.300 1.0080 ; qtot -0.456 19 CG321 1 PEI C5 19 0.00512.0110 ; qtot -0.451 20 HGA2 1 PEIH12 20 0.090 1.0080 ; qtot -0.361 21 HGA2 1 PEIH13 21 0.090 1.0080 ; qtot -0.271 22 CG321 1 PEI C6 22 0.09112.0110 ; qtot -0.180 23 HGA2 1 PEIH14 23 0.090 1.0080 ; qtot -0.090 24 HGA2 1 PEIH15 24 0.090 1.0080 ; qtot -0.000 25 NG301 1 PEI N4 25 -0.81714.0070 ; qtot -0.817 26 CG321 1 PEI C7 26 0.09112.0110 ; qtot -0.726 27 HGA2 1 PEIH16 27 0.090 1.0080 ; qtot -0.636 28 HGA2 1 PEIH17 28 0.090 1.0080 ; qtot -0.546 29 CG321 1 PEI C8 29 0.09112.0110 ; qtot -0.455 30 HGA2 1 PEIH18 30 0.090 1.0080 ; qtot -0.365 31 HGA2 1 PEIH19 31 0.090 1.0080 ; qtot -0.275 32 NG301 1 PEI N5 32 -0.81514.0070 ; qtot -1.090 33 CG321 1 PEI C9 33 0.09112.0110 ; qtot -0.999 34 HGA2 1 PEIH20 34 0.090 1.0080 ; qtot -0.909 35 HGA2 1 PEIH21 35 0.090 1.0080 ; qtot -0.819 36 CG321 1 PEIC10 36 0.00512.0110 ; qtot -0.814 37 HGA2 1 PEIH22 37 0.090 1.0080 ; qtot -0.724 38 HGA2 1 PEIH23 38 0.090 1.0080 ; qtot -0.634 39 NG311 1 PEI N6 39 -0.66914.0070 ; qtot -1.303 40 HGPAM1 1 PEIH24 40 0.300 1.0080 ; qtot -1.003 41 CG321 1 PEIC11 41 0.00412.0110 ; qtot -0.999 42 HGA2 1 PEIH25 42 0.090 1.0080 ; qtot -0.909 43 HGA2 1 PEIH26 43 0.090 1.0080 ; qtot -0.819 44 CG321 1 PEIC12 44 0.09112.0110 ; qtot -0.728 45 HGA2 1 PEIH27 45 0.090 1.0080 ; qtot -0.638 46 HGA2 1 PEIH28 46 0.090 1.0080 ; qtot -0.548 47 CG321 1 PEIC13 47 0.10212.0110 ; qtot -0.446 48 HGA2 1 PEIH29 48 0.090 1.0080 ; qtot -0.356 49 HGA2 1 PEIH30 49 0.090 1.0080 ; qtot -0.266 50 NG321 1
Re: [gmx-users] the a.u. unit in the RMS distribution graph
Thank you Justin, that saved me a lot of time. Best, Lalehan On Sun, Dec 1, 2019 at 3:45 PM Justin Lemkul wrote: > > > On 12/1/19 3:48 AM, Lalehan Ozalp wrote: > > Hello Christian, thank you for providing the patch. However I wonder if > > there is an easier way to convert a.u to frequency - as I need to install > > GROMACS from the start to install the patch. One more thing, I used > version > > 5.0, not 2019, and the patch is written for the version 2019. > > Change the axis label in the .xvg file with a text editor or re-label it > in XmGrace once the data are plotted. You don't need to run the analysis > again with the updated code. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. > -- 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.
Re: [gmx-users] Coulomb and vdW energies
On 12/1/19 5:28 AM, Shreyas Kaptan wrote: Hi. I would not say that it is completely unrealistic/unphysical. Especially, the Electrostatic part. If within two subgroups, you could show that there is systematic repulsive or attractive potential, that could lead to some hypothesis about how they interact (e.g. pushing/pulling). Of course, this is only true of ratios of decomposed energies that are large proportions of the total energy, as smaller portions might not be really significant indicators of strong interactions. I would argue that such an outcome is equally likely to be an indicator of a force field error as it is some real behavior. The problem with all such decomposition is - there is no verifiable target data (QM or empirical) that can tell you which is true. This is why the individual quantities have no meaning. Total interaction energy is a quantity that you can get from QM very easily and is therefore valid target data - CHARMM uses this and the origins of OPLS were the same. Other force fields do not necessarily target such information so the total interaction energy with those models is questionable. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
Re: [gmx-users] the a.u. unit in the RMS distribution graph
On 12/1/19 3:48 AM, Lalehan Ozalp wrote: Hello Christian, thank you for providing the patch. However I wonder if there is an easier way to convert a.u to frequency - as I need to install GROMACS from the start to install the patch. One more thing, I used version 5.0, not 2019, and the patch is written for the version 2019. Change the axis label in the .xvg file with a text editor or re-label it in XmGrace once the data are plotted. You don't need to run the analysis again with the updated code. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com == -- 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.
Re: [gmx-users] Coulomb and vdW energies
Hi. I would not say that it is completely unrealistic/unphysical. Especially, the Electrostatic part. If within two subgroups, you could show that there is systematic repulsive or attractive potential, that could lead to some hypothesis about how they interact (e.g. pushing/pulling). Of course, this is only true of ratios of decomposed energies that are large proportions of the total energy, as smaller portions might not be really significant indicators of strong interactions. Shreyas On Sat, Nov 30, 2019 at 6:47 PM Justin Lemkul wrote: > > > On 11/30/19 3:14 AM, elham wrote: > > Dear all, I want to obtain the coulomb and vdW energies between two > atoms of separate molecules, However the .edr output calculate coulomb > and vdW energies of whole system. There is not any option(like -n .ndx) to > define the the special atoms in the gmx energy command. How can I calculate > the coulomb and vdW energies between the two atoms which are related to two > separate molecules?Best > > Set energygrps in the .mdp file, generate a new .tpr, and use mdrun > -rerun to re-evaluate the energies from an existing trajectory. Note > that decomposition of energy in this way has no physical meaning. Total > interaction energy may be physically realistic if the force field was > specifically parametrized against e.g. QM target data but decomposing > the energy in this way is not meaningful. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > == > > -- > 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. -- Shreyas Sanjay Kaptan -- 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.
Re: [gmx-users] the a.u. unit in the RMS distribution graph
Hello Christian, thank you for providing the patch. However I wonder if there is an easier way to convert a.u to frequency - as I need to install GROMACS from the start to install the patch. One more thing, I used version 5.0, not 2019, and the patch is written for the version 2019. Thank you again, Lalehan On Fri, Nov 29, 2019 at 7:34 PM Christian Blau wrote: > Hello Lalehan and Justin, > > > Thanks for the suggestion! The following patch : > https://gerrit.gromacs.org/c/gromacs/+/14542 does exactly that. > > > Best, > Christian > > On 2019-11-29 14:23, Justin Lemkul wrote: > > > > > > On 11/29/19 7:18 AM, Christian Blau wrote: > >> Hello Lalehan, > >> > >> > >> a.u. stands for "arbitrary units". > >> > >> The rmsd-dist contains a histogram over the distribution of rmsd > values, you can read the a.u. as counts per > >> length-interval. > >> > > > > I would suggest that all histograms that GROMACS produces actually be > labeled reasonably in the code - using a.u. is > > itself arbitrary because it has multiple possible meanings. If it's a > raw histogram, we should be using "Frequency" > > and if normalized, "Probability." > > > > -Justin > > > -- > 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. > -- 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.
