[gmx-users] Calculating atom charges for ester
Dear forum users, I am new to MD and looking for help and a little tutorial how to create a .gro/.pdb file and calculate atom charges for a molecule I can not find online. I have assembled the molecule's .itp file and I seek help how to calculate charges with OPLS. molecule: 4-Methoxyphenyl dichloroacetate -- View this message in context: http://gromacs.5086.x6.nabble.com/Calculating-atom-charges-for-ester-tp5013305.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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] Pressure coupling constants
got you. Thanks again! Santo - K. P. Santo Post doctoral fellow Department of Chemistry University of North Carolina at Chapel Hill Chapel Hill, NC, USA -- View this message in context: http://gromacs.5086.x6.nabble.com/Pressure-coupling-constants-tp5013292p5013308.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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] Calculating atom charges for ester
Hi, Here you go! http://pubs.acs.org/doi/abs/10.1021/jp003919d On Fri, Dec 13, 2013 at 8:42 PM, pp0ta187 p...@live.com wrote: Thank you Justin for a quick response. Although, I can not find the spoken reference in the manual, could you please point in which version is it? -- View this message in context: http://gromacs.5086.x6.nabble.com/Calculating-atom-charges-for-ester-tp5013305p5013310.html Sent from the GROMACS Users Forum mailing list archive at Nabble.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. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- 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] OPLS force field parameters
Thanks Justin. I already added the description in the ffbonded.itp, but nothing is shown in the topol file. I am not sure to put atom names (e.g. C9 C10) or atom type (C C)? However, I tried both and non of them worked. I don't know what I am doing wrong and I appreciate if you could help me resolve my issue. Kind regards, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-us...@gromacs.org Sent: Thursday, December 12, 2013 3:02:22 PM Subject: Re: [gmx-users] OPLS force field parameters On Thu, Dec 12, 2013 at 12:45 PM, Ehsan Sadeghi es...@sfu.ca wrote: Hi gmx users, I try to use OPLS force field for my simulation. I added the following residue to the aminoacids.rtp, but when I generate the topol.top file it does not show the the bond stretching, angle bond, dihedrals. [ NAF ] [ atoms ] C1opls_966 0.3846 1 C2opls_966 0.3846 1 C3opls_966 0.3846 1 C4opls_966 0.3846 1 F17 opls_972 -0.1923 1 F18 opls_972 -0.1923 1 F19 opls_972 -0.1923 1 F20 opls_972 -0.1923 1 F21 opls_972 -0.1923 1 F22 opls_972 -0.1923 1 F23 opls_972 -0.1923 1 F24 opls_972 -0.1923 1 C5opls_966 0.3846 1 C6opls_966 0.3846 1 C7opls_966 0.3846 1 C8opls_966 0.3846 1 F25 opls_972 -0.1923 1 F26 opls_972 -0.1923 1 F27 opls_972 -0.1923 1 F28 opls_972 -0.1923 1 F29 opls_972 -0.1923 1 F30 opls_972 -0.1923 1 F31 opls_972 -0.1923 1 F32 opls_972 -0.1923 1 C9opls_966 0.3846 1 C10 opls_966 0.3846 1 C11 opls_966 0.3846 1 C12 opls_966 0.3846 1 F33 opls_972 -0.1923 1 F34 opls_972 -0.1923 1 F35 opls_972 -0.1923 1 F36 opls_972 -0.1923 1 F37 opls_972 -0.1923 1 F38 opls_972 -0.1923 1 F39 opls_972 -0.1923 1 F40 opls_972 -0.1923 1 C13 opls_966 0.3846 1 C14 opls_966 0.3846 1 C15 opls_967 0.3218 1 C16 opls_966 0.3846 1 F41 opls_972 -0.1923 1 F42 opls_972 -0.1923 1 F43 opls_972 -0.1923 1 F44 opls_972 -0.1923 1 F45 opls_973 -0.1641 1 F46 opls_972 -0.1923 1 F47 opls_972 -0.1923 1 C48 opls_968 0.3228 1 O49 opls_980 -0.2742 1 C50 opls_969 0.401 1 O51 opls_981 -0.2604 1 C52 opls_967 0.3218 1 C53 opls_971 0.3216 1 F55 opls_974 -0.1637 1 F56 opls_974 -0.1637 1 F57 opls_975 -0.1932 1 C58 opls_970 0.4947 1 F59 opls_977 -0.1662 1 F60 opls_977 -0.1662 1 F61 opls_978 -0.3278 1 F62 opls_978 -0.3278 1 F66 opls_976 -0.1649 1 F67 opls_976 -0.1649 1 F68 opls_976 -0.1649 1 S54 opls_979 1.4124 1 O63 opls_982 -0.632 1 O64 opls_982 -0.632 1 O65 opls_982 -0.632 1 Note that assigning all atoms to a single charge group is inappropriate. Surely grompp will warn about this, but you should construct the groups more carefully. snip However, the parameters that we had in topol file are different: [ bonds ] ; aiaj functc0c1c2c3 1 2 1 1 5 1 [ angles ] ; aiajak functc0c1c2 c3 2 1 5 1 2 1 6 1 5 1 6 1 How gromacs can find c0, c1,c2 and c3 from b0, kb, th0, and cth in the ffbonded.itp? I answered this already: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2013-December/086118.html You provide the parameters in ffbonded.itp, grompp goes and finds them. If something is missing, grompp fails. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
Re: [gmx-users] Installing Gromacs 4.6.3 using Cygwin
On 13.12.2013 18:01, chem grad wrote: Thank you so much! Gromacs seems to be installed properly now. but mdrun doesn't work, right? M. -- 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] Installing Gromacs 4.6.3 using Cygwin
On 13.12.2013 21:38, chem grad wrote: I cannot convince cygwin to source the gromacs files properly (well, at least I think that's the problem). When I enter luck into the command line it returns the luck: command not found error message. Also, both commands I have entered (pdb2gmx and mdrun) have returned the following error: /usr/local/gromacs/bin/pdb2gmx.exe: error while loading shared libraries: cyggmxpreprocess-8.dll: cannot open shared object file: No such file or directory Maybe I was not as successful as I thought with the install? No. There are some problems yet to solve. 1) the DLL problem 2) the source problem 3) the tMPI problem of mdrun -- 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] Fw: Error in extendig md run in gromacs
On Sat, Dec 14, 2013 at 10:52 AM, Keerthana S.P Periasamy keerthanas...@yahoo.com wrote: On Saturday, December 14, 2013 10:51 AM, Keerthana S.P Periasamy keerthanas...@yahoo.com wrote: Hai initially I used 4processors for mdrun and due to some power fluctuations i have restatrted my file using 8 processors. I am getting the message as follows. I want to know whether I am correct? #nodes mismatch, current program: 12 checkpoint file: 4 #PME-nodes mismatch, current program: -1 checkpoint file: 0 Gromacs binary or parallel settings not identical to previous run. Continuation is exact, but is not guaranteed to be binary identical. As the note suggest, please supply the checkpoint file to the mdrun command while you are restarting the simulation. The checkpoint file can be supplied with the -cpi FILE.cpt command. Chandan thanks Keerthana -- 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. -- Chandan kumar Choudhury NCL, Pune INDIA -- 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.
