Re: [gmx-users] genbox + python bug?
Thanks for the insights, Mark. It was a 'aprun' issue. When I remove it from the command, everything worked out. -- Marcelo 2015-03-13 14:10 GMT-03:00 Mark Abraham mark.j.abra...@gmail.com: On Fri, Mar 13, 2015 at 5:46 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Hey, I have a python script running gmx commands (version 4.6.7) until the following: *if systype == 'system_1' or systype == 'system_2':genboxcommand = aprun -n 1 genbox_mpi -cs spc216.gro -cp + prefix + .min0.gro -p + prefix + .top -o + prefix + .wat.gro -maxsol + str(water+ion) + os.system(genboxcommand)* And I get the following: *Invalid command line argument:--cp* As you can see, the -cp flag is correct at the command, but inside the script it is read as '--cp' for some reason. Also, other gmx commands run just fine before the crash. This might be a synergetic bug from python and genbox? Does anyone has a suggestion? I'd actually suspect aprun of over-stepping its bounds - I seem to recall some issue like this reported. Anyway, it is useless to run genbox with MPI (and generally useless to do so in a workflow that needs to run mdrun on a machine where aprun would be used, where your compute resources are lying idle while genbox and friends do string processing and file I/O...), so I'd either do my non-mdrun processing separately, or via a version of GROMACS that is not compiled to run with MPI. Perhaps you can get away with just running genbox_mpi on its own, YMMV. Mark -- Marcelo Depólo Polêto B.Sc. Biochemistry - University of Viçosa (Brazil) -- 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. -- Marcelo Depólo Polêto B.Sc. Biochemistry - University of Viçosa (Brazil) -- 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] Dihedral angle autocorrelation function - g_chi function mismatch
Thanks David for the clarifications. I really appreciate it.Atanu On Friday, 13 March 2015 2:07 AM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2015-03-13 00:30, atanu das wrote: Hi David, I have checked both the codes, g_angle.c and g_chi.c, and the same Cos function is used in both the cases (please correct me if I am wrong). g_angle analysis: I have used the following command to calculate the average autocorrelation function (ACF) over all the backbone phi psi dihedral angles given in the index file. The phi-psi definition I use in the index file is the usual description of dihedral angles i.e. C-N-CA-C and N-CA-C-N. g_angle -f final.xtc -n phi-psi.ndx -oc dihcorr.xvg -type dihedral -avercorr g_chi analysis: I have used the following command to estimate the autocorrelation function of individual dihedral angles and then estimated the average autocorrelation function to compare with the previous result. g_chi -s md.tpr -f final.xtc -corr -phi -psi The two curves (average ACFs calculated by two procedure) show almost similar behavior (tried to attach the figure file, but couldn't due to size limit). The slightly faster relaxation time obtained from g_chi may be attributed to the phi-psi description in-built in g_chi analysis (H-N-CA-C and N-CA-C-O). Is there a way to calculate ACF using the formula you described in your Biophysical Journal 97 article (Eq. 1)? ThanksAtanu I think g_chi does exactly that. On Thursday, 12 March 2015 6:12 PM, atanu das samr...@yahoo.co.in wrote: HiDavid, Ihave checked both the codes, g_angle.c and g_chi.c, and the same Cos function is usedin both the cases (please correct me if I am wrong). I am sending this figureto you (to all others) to explain my approach clearly. Ihave simulated the system for 1 microsecond and chosen the default i.e. half ofthe simulations length (500 ns) for ACF analysis. g_angleanalysis: I have used the following command to calculate the averageautocorrelation function (ACF) over all the backbone phi psi dihedralangles given in the index file. The phi-psi definition I used in the index fileis the usual description of dihedral angles i.e. C-N-CA-C and N-CA-C-N. g_angle-f final.xtc -n phi-psi.ndx -oc dihcorr.xvg -type dihedral -avercorr g_chianalysis: I have used the following command to estimate the autocorrelationfunction of individual dihedral angles and then estimated the averageautocorrelation function to compare with the previous result. The two curvesshow almost similar beha vior. The slightly faster relaxation time obtained fromg_chi (green line) may be attributed to the phi-psi description in-built in g_chianalysis (H-N-CA-C and N-CA-C-O) g_chi-s md.tpr -f final.xtc -corr -phi -psi Isthere a way to calculate ACF using the formula you described in your BiophysicalJournal 97 article (Eq. 1)? ThanksAtanu On Thursday, 12 March 2015 2:19 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2015-03-12 19:03, atanu das wrote: Hi again, Just to add a note --- It seems that g_angle can also calculate the dihedral angle autocorrelation function with the option -oc. Does this program use the same functional form as g_chi i.e. is the functions defined as --- C(t) = cos(theta(tau)) cos(theta(tau+t)) I don't think so, but please check the source code if unsure. ThanksAtanu On Wednesday, 11 March 2015 9:13 PM, atanu das samr...@yahoo.co.in wrote: Hi All, As Prof. David van der Spoel referred in the last communication about how the dihedral angle autocorrelation function is calculated via the program g_chi, I have a query regarding the differences that I found between the function mentioned in the article (Biophys. J. 72 pp. 2032-2041 (1997)) and the function used by the program g_chi. According to the article, the dihedral angle autocorrelation function is defined as: C(t) = cos[theta(tau)-theta(tau+t)] . (Eq. 1 of the article) However, the g_chi program uses the function: C(t) = cos(theta(tau)) cos(theta(tau+t)) . (Eq. 2) So, apparently the g_chi program uses a different function. Am I correct? Is there a way around it? I mean is there a way to estimate C(t) using the function given in the article (Eq. 1)? ThanksAtanu -- 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 -- 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
Re: [gmx-users] genbox + python bug?
On Fri, Mar 13, 2015 at 5:46 PM, Marcelo Depólo marcelodep...@gmail.com wrote: Hey, I have a python script running gmx commands (version 4.6.7) until the following: *if systype == 'system_1' or systype == 'system_2':genboxcommand = aprun -n 1 genbox_mpi -cs spc216.gro -cp + prefix + .min0.gro -p + prefix + .top -o + prefix + .wat.gro -maxsol + str(water+ion) + os.system(genboxcommand)* And I get the following: *Invalid command line argument:--cp* As you can see, the -cp flag is correct at the command, but inside the script it is read as '--cp' for some reason. Also, other gmx commands run just fine before the crash. This might be a synergetic bug from python and genbox? Does anyone has a suggestion? I'd actually suspect aprun of over-stepping its bounds - I seem to recall some issue like this reported. Anyway, it is useless to run genbox with MPI (and generally useless to do so in a workflow that needs to run mdrun on a machine where aprun would be used, where your compute resources are lying idle while genbox and friends do string processing and file I/O...), so I'd either do my non-mdrun processing separately, or via a version of GROMACS that is not compiled to run with MPI. Perhaps you can get away with just running genbox_mpi on its own, YMMV. Mark -- Marcelo Depólo Polêto B.Sc. Biochemistry - University of Viçosa (Brazil) -- 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] diisopropylethylene topology
Dear All, Does anyone has the itp file for diisopropylethylene? It would be very helpful if you can share. Many thanks in advance. Regards, Quy -- 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] Placing system at the centre of the box.
Hi all, I am trying to study wetting of water on Graphene oxide(GO). My structure has functional group in form of epoxide group on one side of the Graphene sheet. Also I have added water molecules in form of spherical droplet on the same side of the sheet. I used the following commands to generate .gro. editconf -f GO.pdb -o conf.gro -box 3 3 3 -angles 90 90 90 -c - Read 260 atoms No velocities found system size : 1.845 1.562 1.523 (nm) center : 0.985 0.828 0.380 (nm) box vectors : 0.000 0.000 0.000 (nm) box angles : 0.00 0.00 0.00 (degrees) box volume : 0.00 (nm^3) shift : 0.515 0.672 1.120 (nm) new center : 1.500 1.500 1.500 (nm) new box vectors : 3.000 3.000 3.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 27.00 (nm^3) My question is, what is this* center* and how is it calculated by editconf? When I see conf.gro in VMD, I don't actually see my system at the geometric center of the box. -- Rajan Kumar Indian Institute of Technology, Guwahati -- 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] Dihedral angle autocorrelation function - g_chi function mismatch
On 2015-03-13 00:30, atanu das wrote: Hi David, I have checked both the codes, g_angle.c and g_chi.c, and the same Cos function is used in both the cases (please correct me if I am wrong). g_angle analysis: I have used the following command to calculate the average autocorrelation function (ACF) over all the backbone phi psi dihedral angles given in the index file. The phi-psi definition I use in the index file is the usual description of dihedral angles i.e. C-N-CA-C and N-CA-C-N. g_angle -f final.xtc -n phi-psi.ndx -oc dihcorr.xvg -type dihedral -avercorr g_chi analysis: I have used the following command to estimate the autocorrelation function of individual dihedral angles and then estimated the average autocorrelation function to compare with the previous result. g_chi -s md.tpr -f final.xtc -corr -phi -psi The two curves (average ACFs calculated by two procedure) show almost similar behavior (tried to attach the figure file, but couldn't due to size limit). The slightly faster relaxation time obtained from g_chi may be attributed to the phi-psi description in-built in g_chi analysis (H-N-CA-C and N-CA-C-O). Is there a way to calculate ACF using the formula you described in your Biophysical Journal 97 article (Eq. 1)? ThanksAtanu I think g_chi does exactly that. On Thursday, 12 March 2015 6:12 PM, atanu das samr...@yahoo.co.in wrote: HiDavid, Ihave checked both the codes, g_angle.c and g_chi.c, and the same Cos function is usedin both the cases (please correct me if I am wrong). I am sending this figureto you (to all others) to explain my approach clearly. Ihave simulated the system for 1 microsecond and chosen the default i.e. half ofthe simulations length (500 ns) for ACF analysis. g_angleanalysis: I have used the following command to calculate the averageautocorrelation function (ACF) over all the backbone phi psi dihedralangles given in the index file. The phi-psi definition I used in the index fileis the usual description of dihedral angles i.e. C-N-CA-C and N-CA-C-N. g_angle-f final.xtc -n phi-psi.ndx -oc dihcorr.xvg -type dihedral -avercorr g_chianalysis: I have used the following command to estimate the autocorrelationfunction of individual dihedral angles and then estimated the averageautocorrelation function to compare with the previous result. The two curvesshow almost similar beha vior. The slightly faster relaxation time obtained fromg_chi (green line) may be attributed to the phi-psi description in-built in g_chianalysis (H-N-CA-C and N-CA-C-O) g_chi-s md.tpr -f final.xtc -corr -phi -psi Isthere a way to calculate ACF using the formula you described in your BiophysicalJournal 97 article (Eq. 1)? ThanksAtanu On Thursday, 12 March 2015 2:19 PM, David van der Spoel sp...@xray.bmc.uu.se wrote: On 2015-03-12 19:03, atanu das wrote: Hi again, Just to add a note --- It seems that g_angle can also calculate the dihedral angle autocorrelation function with the option -oc. Does this program use the same functional form as g_chi i.e. is the functions defined as --- C(t) = cos(theta(tau)) cos(theta(tau+t)) I don't think so, but please check the source code if unsure. ThanksAtanu On Wednesday, 11 March 2015 9:13 PM, atanu das samr...@yahoo.co.in wrote: Hi All, As Prof. David van der Spoel referred in the last communication about how the dihedral angle autocorrelation function is calculated via the program g_chi, I have a query regarding the differences that I found between the function mentioned in the article (Biophys. J. 72 pp. 2032-2041 (1997)) and the function used by the program g_chi. According to the article, the dihedral angle autocorrelation function is defined as: C(t) = cos[theta(tau)-theta(tau+t)] . (Eq. 1 of the article) However, the g_chi program uses the function: C(t) = cos(theta(tau)) cos(theta(tau+t)) . (Eq. 2) So, apparently the g_chi program uses a different function. Am I correct? Is there a way around it? I mean is there a way to estimate C(t) using the function given in the article (Eq. 1)? ThanksAtanu -- 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 -- 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] boron atom
OK, thanks Justin. Best regards On Fri, Mar 13, 2015 at 1:52 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/12/15 9:16 AM, Faezeh Pousaneh wrote: Hi, Does any one know which force filed contains 'Boron' atom? I need it for my simulation, molecule sodium tetraphenylborate. None of the built-in force fields have boron. So either you need to obtain parameters that are published or derive them yourself. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] problem in defining protonation state of amino acids
Hi everyone, I want to do a constant pH simulation of my protein using CHARMM36. I calculated protonation state of various amino acid at required pH using H++ server. However when trying to run pdb2gmx got fatal error Atom HB3 in residue SER 3 was not found in rtp entry SER with 11 atoms while sorting atoms. I can remove the error by adding -ignh but my concerned is this may change the protonation state. Please help me with your valuable suggestion. Thanks for your time and effort. Tushar Ranjan Moharana B. Tech, NIT Warangal Ph D Student, CCMB -- 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] query regarding coarse grained simulation of a peripheral membrane protein
Hi, How do i generate a topology file of a peripherally attached dimeric protein with a homogenous lipid bilayer using coarse grained approach? i have concatenated the coarse grained structure of lipids and protein prior to this. -- *Best,* *Antara* -- J.R.F.(Project) Systems Biology Group CSIR - Institute of Genomics Integrative Biology South Campus, New Delhi-110020 M:+91-9717970040 -- -- 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] problem in defining protonation state of amino acids
On 3/13/15 8:08 AM, Tushar Ranjan Moharana wrote: Hi everyone, I want to do a constant pH simulation of my protein using CHARMM36. I Just for clarity fixed protonation and constant pH are not synonymous. Natively, GROMACS does not do constant pH simulations, though I believe some groups have developed software to do this. calculated protonation state of various amino acid at required pH using H++ server. However when trying to run pdb2gmx got fatal error Atom HB3 in residue SER 3 was not found in rtp entry SER with 11 atoms while sorting atoms. I can remove the error by adding -ignh but my concerned is this may change the protonation state. Please help me with your valuable suggestion. As the name implies, HB3 is attached to CB. The force field expects HB1 and HB2, but your coordinate file doesn't adhere to that nomenclature. Renaming the offending HB3 or using -ignh are both fine. HB* are not titratable (under normal circumstances, and moreover the force field won't support any weird anionic CB form of SER) so they don't factor into your setup. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] genbox + python bug?
Hey, I have a python script running gmx commands (version 4.6.7) until the following: *if systype == 'system_1' or systype == 'system_2':genboxcommand = aprun -n 1 genbox_mpi -cs spc216.gro -cp + prefix + .min0.gro -p + prefix + .top -o + prefix + .wat.gro -maxsol + str(water+ion) + os.system(genboxcommand)* And I get the following: *Invalid command line argument:--cp* As you can see, the -cp flag is correct at the command, but inside the script it is read as '--cp' for some reason. Also, other gmx commands run just fine before the crash. This might be a synergetic bug from python and genbox? Does anyone has a suggestion? -- Marcelo Depólo Polêto B.Sc. Biochemistry - University of Viçosa (Brazil) -- 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.
