[gmx-users] lincs warning
Sent from Yahoo Mail on Android - Forwarded Message - From: "Afsane Farhadi" To: "gromacs.org_gmx-users@maillist.sys.kth.se" Cc: Sent: Mon, Apr 27, 2020 at 3:52 PM Subject: lincs warning Hi users I have two types of molecules ,methane and carbondioxide. i optimized them by gaussian calculation and i edited the atom name and residue by vim. I extracted the epsilon and sigma parameter from the articles . i generated a box of 500 methane molecules and 62 carbondioxide by insert-molecules. I have done energy minimization and its ok (potential energy is -2e+03).when i was running npt.mdp the lincs warning was showed( bond rotate more than 30 degree)I need help thanks alot for your quick answers .the topology and npt.mdp is:#include "oplsaa.ff/forcefield.itp" [ atomtypes ] CO C01 12.0110 0.775 A 2.75700E-01 2.33790E-01 OC O01 15.99940 -0.388 A 3.03300E-01 6.69120E-01 opls_801 H801 1.0080 0.125 A 1.48720E-01 0.65688E-01 opls_803 H803 1.0080 0.125 A 1.48720E-01 0.65688E-01 opls_804 H804 1.0080 0.125 A 1.48720E-01 0.65688E-01 opls_800 C800 12.0110 -0.502 A 1.90820E-01 4.57729E-01 opls_802 H802 1.0080 0.125 A 1.48720E-01 0.65688E-01 [ moleculetype ] ; Name nrexcl CH4 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_800 1 H C 1 -0.5020 12.0110 2 opls_801 1 H H 1 0.1250 1.0080 3 opls_802 1 H H 1 0.1250 1.0080 4 opls_803 1 H H 1 0.1250 1.0080 5 opls_804 1 H H 1 0.1250 1.0080 [ bonds ] 2 1 1 0.1090 138490.400 3 1 1 0.1090 138490.400 4 1 1 0.1090 138490.400 5 1 1 0.1090 138490.400 [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 3 1 109.500 146.440 2 1 4 1 109.500 146.440 2 1 5 1 109.500 146.440 3 1 4 1 109.500 146.440 4 1 5 1 109.500 146.440 3 1 5 1 109.500 146.440 [ moleculetype ] ; Name nrexcl CAR 3 [atoms] ; nr type resnr residue atom cgnr charge mass 1 CO 1 CAR CO 1 0.775 12.0110 2 OC 1 CAR OC 1 -0.388 15.9994 3 OC 1 CAR OC 1 -0.388 15.9994 [ bonds ] 1 2 1 0.11620 844300 1 3 1 0.11620 844300 [angles] ; ai aj ak funct c0 c1 c2 c3 2 1 3 1 180 451.9 [system]: co2 in methane [molecules] CH4 500 CAR 62 Sent from Yahoo Mail on Android -- 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] lincs warning
Hi gromacs users I generated a mixed box of methane and carbondioxide with insert-molecules (500 methane+62carbondioxide) . The pdb file of methane and carbondioxide are optimized and the energy minimization of mixed gas is ok (potential energy is about -2e+03))but when I want to run a npt run ,the lincs warning are showing( bond rotate more than 30 degree).I repeated energy minimization but it didn't work right Can any body help me please? Sent from Yahoo Mail on Android -- 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] energy minimization
hi friends I generated a box of mixed gas with gmx insert-moleculesI ran an energy minimizing. the potential energy is 4.05e+07 and maximum force is 1.25e+03.I used different algorithm likes cg and steep for minimization. what do I have to do untill my system potential energy has negative value??I need a information about energy minimizing and potential energy. I know that positive value of potential energy means the intermolecular interaction is weaker than intramolecular interaction but I don't know how I can control this matter. please help Sent from Yahoo Mail on Android -- 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] energy minimizing
hi friends I generated a box of mixed gas with gmx insert-moleculesI ran an energy minimizing. the potential energy is 4.05e+07 and maximum force is 1.25e+03.I used different algorithm likes cg and steep for minimization. what do I have to do untill my system potential energy has negative value??I need a information about energy minimizing and potential energy. I know that positive value of potential energy means the intermolecular interaction is weaker than intramolecular interaction but I don't know how I can control this matter. please help Sent from Yahoo Mail on Android -- 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] topology of co2
hi allI want to download a topology of co2 by opls as forcefield, but many servers doesn't answer(like ligpargen and tppmktop). how can I find a topology for this molecule? Sent from Yahoo Mail on Android -- 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] positive potential energy
hi all I generated a box 4×4×4 (nm) with 100 molecules methyldiethanolamine by insert-molecules , forcefield is opls . after energy minimization the potential energy decreased but had a positive value . is my simulation wrong ? help me please Sent from Yahoo Mail on Android -- 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] potential energy doesn't have negative value
thank you so much Mr.justin Sent from Yahoo Mail on Android On Sun, Mar 15, 2020 at 3:38, Justin Lemkul wrote: On 3/14/20 8:05 PM, Afsane Farhadi wrote: > what do I have to do for solving this mater? I want to use a opls as > forcefield. how can I find that forcefield for methyldiethanolamine? http://zarbi.chem.yale.edu/ligpargen/ -Justin > Sent from Yahoo Mail on Android > > On Sun, Mar 15, 2020 at 3:29, Justin Lemkul wrote: > > On 3/14/20 7:15 PM, Afsane Farhadi wrote: >> I generate a box of 100 molecules of methyldiethanolamine with >> insert-molecules command .I downloaded its itp file from ATB server. I think >> that forcefield is gromos . after an energy minimization the potential >> energy is positive. the mdp file is attached. > The mailing list does not accept attachments. > > ATB does produce GROMOS-compatible force fields, but it is always up to > the user to determine if the parameters are suitable. A positive > potential energy means that the intermolecular interactions are weak > compared to the intramolecular (bonded) interactions. You can use gmx > energy or look in the .log file to see the various contributions to the > total potential energy. > > -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] potential energy doesn't have negative value
what do I have to do for solving this mater? I want to use a opls as forcefield. how can I find that forcefield for methyldiethanolamine? Sent from Yahoo Mail on Android On Sun, Mar 15, 2020 at 3:29, Justin Lemkul wrote: On 3/14/20 7:15 PM, Afsane Farhadi wrote: > I generate a box of 100 molecules of methyldiethanolamine with > insert-molecules command .I downloaded its itp file from ATB server. I think > that forcefield is gromos . after an energy minimization the potential energy > is positive. the mdp file is attached. The mailing list does not accept attachments. ATB does produce GROMOS-compatible force fields, but it is always up to the user to determine if the parameters are suitable. A positive potential energy means that the intermolecular interactions are weak compared to the intramolecular (bonded) interactions. You can use gmx energy or look in the .log file to see the various contributions to the total potential energy. -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.
[gmx-users] potential energy doesn't have negative value
I generate a box of 100 molecules of methyldiethanolamine with insert-molecules command .I downloaded its itp file from ATB server. I think that forcefield is gromos . after an energy minimization the potential energy is positive. the mdp file is attached. Sent from Yahoo Mail on Android-- 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] pressure fluctuation and actual density
hiI want to simulate a box of methyldiethanol amine and see the actual density . I set 100 amine molecules in a cubic box 4×4×4 (nm^3)I first used energy minimization for 400ps . then I used npt for 2ns. I saw a lot fluctuation in pressure .pressure is 1bar.I used Rahman barostat. is my procedure correct? what is the suitable fluctuation around pressure?what is the number of compressibility isotherm of MDEA? Sent from Yahoo Mail on Android -- 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] (no subject)
afsane_farh...@yahoo.com Sent from Yahoo Mail on Android -- 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.
