[gmx-users] pdo files
Dear all user,I want to make a file "pdo-files.dat". I don't know what must i do. can anybody help me?Many thanks,Mahdavi -- 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] g_wham error
Dear Justin,I want to make a .pdo files but i don't know what dose mean 'Umbrella positions' in following: UMBRELLA 3.0 Component selection: 0 0 1 nSkip 1 Ref. Group 'TestAtom' Nr. of pull groups 2 Group 1 'GR1' Umb. Pos. 5.0 Umb. Cons. 1000.0 The number of pull groups, umbrella positions, force constants, and names may (of course) differ.is it mean the selected numbers for 'pullf-files.dat'(lists the names of the .tpr files of each window)?many thanks,Mahdavi -- 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] g_wham error
Dear Justin,I want to calculated the PMF for passing a drug from Z-coordination of DPPc bilayer, at the end of calculations i gave a fatal error as following:Fatal error: Found pull geometry 'position' and more than 1 pull dimension (3). Hence, the pull potential does not correspond to a one-dimensional umbrella potential.what must i do exactly? I want to give PMF along the Z axis.many thanks,Mahdavi -- 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] Error
Dear David van der Spoel,which plot must be check? I used this command "g_hbond -f md.xtc -s md.tpr -n index.ndx -num DrugwithWater.xvg" and i get a data point in the end of run of this command and i used it for report. I want to report this data point and it's error. what must i do?many thanks, Mrs. Mahdavi -- 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] Error in number og H-bond
Dear Justin,I calculated the H-bond with g_hbond. I want to calculate the error of H-bond, what must i do?many thanks,Mrs. Mahdavi -- 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] Tilt angle
Dear Justin,I want to calculate the tilt angle of DPPC, which command must be used?Thank you,Mrs.Mahdavi On Thursday, March 12, 2015 10:49 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: umbrella sampling tutorial (Justin Lemkul) 2. Re: trajectory film (Justin Lemkul) 3. boron atom (Faezeh Pousaneh) 4. boron atom (Faezeh Pousaneh) 5. Re: Dihedral angle autocorrelation function - g_chi function mismatch (atanu das) 6. Re: Dihedral angle autocorrelation function - g_chi function mismatch (atanu das) 7. Re: Dihedral angle autocorrelation function - g_chi function mismatch (David van der Spoel) -- Message: 1 Date: Thu, 12 Mar 2015 07:50:17 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] umbrella sampling tutorial Message-ID: 55017d79.40...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 3/12/15 2:41 AM, Ming Tang wrote: Dear Justin, The results turned out that the COM distance between them is the same over time, seems that both Chain_A and Chain_B had been pulled by the same force in the same direction, which is different from the tutorial. Switch Chain_A and Chain_B in the .mdp file. -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 == -- Message: 2 Date: Thu, 12 Mar 2015 07:51:20 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] trajectory film Message-ID: 55017db8.5080...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 3/12/15 2:23 AM, mah maz wrote: Dear all, I have a question probably not related to this mailing list! I want to see a film of an output trajectory via VMD. I tried the .trr file by the appropriate format in VMD, it shows that the frames are being constructed and rendering is complete but nothing can be seen. Is there a problem with my .trr file? Can anyone help me in this regard? There is a VMD mailing list that is more appropriate for this question. Make sure you load the initial coordinates first, then load the .trr as data for those coordinates. You can't just load a .trr (or any trajectory) by itself. -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 == -- Message: 3 Date: Thu, 12 Mar 2015 14:16:50 +0100 From: Faezeh Pousaneh fpoosa...@gmail.com To: gmx-users gmx-us...@gromacs.org, gromacs.org_gmx-users-requ...@maillist.sys.kth.se, gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] boron atom Message-ID: cajtntaua+xgzyx7hzc31t1dr2ucjbxggdmryjlffkararrf...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi, Does any one know which force filed contains 'Boron' atom? I need it for my simulation, molecule sodium tetraphenylborate. Best regards -- Message: 4 Date: Thu, 12 Mar 2015 14:16:50 +0100 From: Faezeh Pousaneh fpoosa...@gmail.com To: gmx-users gmx-us...@gromacs.org, gromacs.org_gmx-users-requ...@maillist.sys.kth.se, gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] boron atom Message-ID: cajtntaua+xgzyx7hzc31t1dr2ucjbxggdmryjlffkararrf...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi, Does any one know which force filed contains 'Boron' atom? I need it for my simulation, molecule sodium tetraphenylborate. Best regards -- Message: 5 Date: Thu, 12 Mar 2015 18:03:51 + (UTC) From:
[gmx-users] NVT step
Dear Justin,I studied your toturial (KALP15 in DPPC).I'm simulating a drug at dppc, at nvt step i used this command: mdrun -deffnm nvt -v , but i gave this error: Fatal error: 1 particles communicated to PME node 1 are more than 2/3 times the cut-off outof the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. For more information and tips for troubleshooting, please check theGROMACS website at http://www.gromacs.org/Documentation/Errors what must i do? Many thanks, Mrs. Mahdavi -- 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] ngmx tools
Dear Justin,I'm using the GROMACS 5.0 , it seems that there isn't ngmx tool in this version, would you please help me? Which command(s) must be used for visualization?Thanks,Mrs.Mahdavi -- 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] PME update
Dear Justin,I studied KALP15 in DPPC, would you please help me? I want to know how often PME was updated in this tutorial? every 10th time step? How can i know?Many thanks,Mrs.Mahdavi On Sunday, January 18, 2015 9:57 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Decomposing the long range term of interaction energy (Diogo Martins de =?UTF-8?Q?S=C3=A1?=) 2. Re: Decomposing the long range term of interaction energy (David van der Spoel) 3. adding new residue (fatemeh ramezani) -- Message: 1 Date: Sun, 18 Jan 2015 06:07:41 -0700 From: Diogo Martins de =?UTF-8?Q?S=C3=A1?= sadi...@mol.bio.br To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Decomposing the long range term of interaction energy Message-ID: 20150118060741.9fb2472ef9329f096e098461db973df3.618ccf3321@email14.secureserver.net Content-Type: text/plain; charset=utf-8 I've been reading many tentatives of breaking down the long range term of interaction, but have not found a feedback if any actually worked. Is there a working method of achieving this? Att. Diogo -- Message: 2 Date: Sun, 18 Jan 2015 15:48:37 +0100 From: David van der Spoel sp...@xray.bmc.uu.se To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Decomposing the long range term of interaction energy Message-ID: 54bbc7c5.9060...@xray.bmc.uu.se Content-Type: text/plain; charset=windows-1252; format=flowed On 2015-01-18 14:07, Diogo Martins de S? wrote: I've been reading many tentatives of breaking down the long range term of interaction, but have not found a feedback if any actually worked. Is there a working method of achieving this? Att. Diogo We have done it and published the method in the supporting info of this paper http://pubs.acs.org/doi/abs/10.1021/ct400404q How useful it is depends on your system I guess. Paper is interesting too :). -- 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 -- Message: 3 Date: Sun, 18 Jan 2015 18:26:27 + (UTC) From: fatemeh ramezani fr_...@yahoo.com To: gmx-users-ow...@gromacs.org gmx-users-ow...@gromacs.org, gmx-users-requ...@gromacs.org gmx-users-requ...@gromacs.org, gmx-us...@gromacs.org gmx-us...@gromacs.org Subject: [gmx-users] adding new residue Message-ID: 488796205.2916602.1421605587462.javamail.ya...@jws10640.mail.bf1.yahoo.com Content-Type: text/plain; charset=UTF-8 Dear gmx-usersI want to simulate collagen molecule by gromacs. I produce hydroxyprolin parameter by swissparam site: ; ; Built itp for zinc_901791.mol2 ;??? by user vzoete Mon Jan 12 11:37:34 CET 2015 ; ; [ atomtypes ] ; name at.num? mass?? charge? ptype??? sigma??? epsilon CR? 6?? 12.0110? 0.0? A 0.387541??? 0.230120? HCMM??? 1??? 1.0079? 0.0? A 0.235197??? 0.092048 CO2M??? 6?? 12.0110? 0.0? A 0.356359??? 0.292880? O2CM??? 8?? 15.9994? 0.0? A 0.302905??? 0.502080? OR? 8?? 15.9994? 0.0? A 0.315378??? 0.636386? HOR 1??? 1.0079? 0.0? A 0.040001??? 0.192464? NRP 7?? 14.0067? 0.0? A 0.329632??? 0.836800 HNRP??? 1??? 1.0079? 0.0? A 0.040001??? 0.192464? [ pairtypes ] ;? i j??? func sigma1-4?? epsilon1-4 ; THESE ARE 1-4 INTERACTIONS CR?? CR 1? 0.338541??? 0.041840 CR?? HCMM?? 1? 0.286869??? 0.062059 CR?? CO2M?? 1? 0.347450??? 0.110698 CR?? O2CM?? 1? 0.320723??? 0.144938 CR?? OR 1? 0.326960??? 0.163176 CR?? HOR??? 1? 0.189271??? 0.089737 CR?? NRP??? 1? 0.334087??? 0.187114 CR?? HNRP?? 1? 0.189271??? 0.089737 [ moleculetype ] ; Name nrexcl zinc_901791 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass ?? 1 CR?? 1? LIG C1? 1? 0.? 12.0110 ?? 2 CR?? 1? LIG C2? 2? 0.2800? 12.0110 ?? 3 HCMM 1? LIG H1? 3? 0.?? 1.0079 ?? 4 CR?? 1? LIG C3? 4? 0.5030? 12.0110 ?? 5 CR?? 1? LIG C4? 5? 0.3970? 12.0110 ?? 6 HCMM 1? LIG H2? 6? 0.?? 1.0079 ?? 7 CO2M 1? LIG C5? 7? 0.9060? 12.0110 ?? 8 O2CM 1? LIG O1? 8
Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 129, Issue 32
Dear Justin,I want to use GridMAT-MD program for last 70 ns my simulation, wat must i do?Many thanks,Mrs. Mahdavi On Friday, January 9, 2015 5:21 AM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: Error : Atomtype not found (Justin Lemkul) 2. rotating triclinic box (felipe zapata) 3. Re: rotating triclinic box (Tsjerk Wassenaar) 4. compiling issue (?ric Germaneau) 5. Re: compiling issue (?ric Germaneau) 6. Re: RDF plot with large g(r) values (Kester Wong) -- Message: 1 Date: Thu, 08 Jan 2015 10:27:26 -0500 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Error : Atomtype not found Message-ID: 54aea1de.6020...@vt.edu Content-Type: text/plain; charset=windows-1252; format=flowed On 1/8/15 10:14 AM, protim chakraborti wrote: Respected Dr. Lemkul Thanks for the suggestion. I have checked the ffnonbonded.itp and found that copper is entered out there in the following form and format ; Ions and noble gases (useful for tutorials) Cu2+ 29 63.54600 2.00 A 2.08470e-01 4.76976e+00 Ar 18 39.94800 0.00 A 3.41000e-01 2.74580e-02 would this be not be suffice or i need to add Cu separately? or may be I have to run starting from pdb2gmx itself! Those parameters are not CHARMM parameters. They appear to have been copied over from OPLS-AA, which had several ions removed due to unknown origins (as was Ar). Do not use these parameters for a CHARMM simulation. I recommend that they be removed entirely, as we did with our CHARMM36 port. -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 == -- Message: 2 Date: Thu, 8 Jan 2015 16:25:03 -0500 From: felipe zapata tifonza...@gmail.com To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] rotating triclinic box Message-ID: CA+AeLgSe5Pj8iRcgaFU9-E4zx7830PK9p=oatuudnfa9zrm...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi all, I have a triclinic box containing several chains of a biopolymer with the following crystal information: CRYST1 115.000 75.000 75.000 80.37 118.08 114.80 P 1 1 I want to apply a semiistropic pressure coupling orthogonal to the chains (XY plane), but unfortunately the strands of the polymer are oriented along the x-axis instead of the z-axis. How can I change the orientation of the box in such a way that the strand are orientated along the z-axis? it means I want to rotate the triclinic box swapping the x and z axes. Best, Felipe -- Message: 3 Date: Thu, 8 Jan 2015 22:39:03 +0100 From: Tsjerk Wassenaar tsje...@gmail.com To: Discussion list for GROMACS users gmx-us...@gromacs.org Subject: Re: [gmx-users] rotating triclinic box Message-ID: cabze1sjrmvh-hgwdrtnk_gkrs3_f5mopcl1k3dce+qrt79s...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi Felipe, Rotate 90 degrees around y: editconf -rotate 0 90 0 Cheers, Tsjerk On Jan 8, 2015 10:32 PM, felipe zapata tifonza...@gmail.com wrote: Hi all, I have a triclinic box containing several chains of a biopolymer with the following crystal information: CRYST1 115.000 75.000 75.000 80.37 118.08 114.80 P 1 1 I want to apply a semiistropic pressure coupling orthogonal to the chains (XY plane), but unfortunately the strands of the polymer are oriented along the x-axis instead of the z-axis. How can I change the orientation of the box in such a way that the strand are orientated along the z-axis? it means I want to rotate the triclinic box swapping the x and z axes. Best, Felipe -- 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
[gmx-users] GridMAT-MD
Dear Justin,I want to use?GridMAT-MD program?for last 70 ns my simulation, wat must i do?Many thanks,Mrs. Mahdavi -- 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] Electrostatic potential
Dear justin, I want to calculated electrostatic potential (dipoles potential), but i don't know what command must be used, would you please help me? Many thanks, Mrs. Mahdavi -- 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] Electrostatic potential
Dear justin, I want to calculated electrostatic potential (dipoles potential), but i don't know what command must be used, would you please help me? this potential must be like this file that attached. Many thanks, Mrs. Mahdavi On Tuesday, January 6, 2015 12:13 AM, asasa qsqs sanaz_d...@yahoo.com wrote: Dear justin, I want to calculated electrostatic potential (dipoles potential), but i don't know what command must be used, would you please help me? Many thanks, Mrs. Mahdavi -- 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] gromacs.org_gmx-users Digest, Vol 129, Issue 4
Dear justin, I want to calculate the electrostatic potential of pure DPPC with this command g_potential -f md.trr -s md.tpr -n dppc.ndx -sl 70 -o electrostatic.xvg but i gave negative value for it that is not in agreement with another simulations. content of electrostatic.xvg is : # This file was created Fri Jan 2 06:59:44 2015 # by the following command: # g_potential -f md.trr -n dppc.ndx -s md.tpr -d z -sl 70 -o electrostatic.xvg # # g_potential is part of G R O M A C S: # # Gromacs Runs On Most of All Computer Systems # @title Electrostatic Potential @xaxis label Box (nm) @yaxis label Potential (V) @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend DPPC 0 -0 0.1020072937011719 -2.567502819917437e-07 0.2040145874023437 -5.135005644617221e-06 0.3060218811035156 -4.947257004377959e-05 0.4080291748046875 -0.0003370328865105846 0.5100364685058594 -0.001842456075442605 0.6120437622070312 -0.008000900456833342 0.7140510559082031 -0.0277002585097313 0.816058349609375 -0.07850842775718628 0.9180656433105469 -0.1869234659171869 1.020072937011719 -0.3819110421478191 1.122080230712891 -0.6821675855578936 1.224087524414062 -1.084356581618383 1.326094818115234 -1.563908413892375 1.428102111816406 -2.088089675203653 1.530109405517578 -2.622860581236976 1.63211669921875 -3.136185314266401 1.734123992919922 -3.600551094919505 1.836131286621094 -3.988238825132194 1.938138580322265 -4.278617107110116 2.040145874023438 -4.469604973139271 2.142153167724609 -4.577608951258815 2.244160461425781 -4.629402873791392 2.346167755126953 -4.649992367693026 2.448175048828125 -4.656826483858561 2.550182342529297 -4.658976705591106 2.652189636230469 -4.659532283703276 2.75419692993164 -4.659610386590746 2.856204223632812 -4.659623050260158 2.958211517333984 -4.659629776578899 3.060218811035156 -4.659632940486518 3.162226104736328 -4.659633456656731 3.2642333984375 -4.659633732123568 3.366240692138672 -4.659634007590405 3.468247985839843 -4.659634283057242 3.570255279541016-4.65963455852408 3.672262573242187 -4.659634737709559 3.774269866943359 -4.659634242925521 3.876277160644531 -4.659632143452044 3.978284454345703 -4.659629867461843 4.080291748046875 -4.659672875799365 4.182299041748046 -4.659850308951451 4.284306335449219 -4.659936339019628 4.386313629150391 -4.659331951664936 4.488320922851562-4.65658309018609 4.590328216552734 -4.646515258536495 4.692335510253906 -4.616826878885218 4.794342803955078 -4.546972187682989 4.896350097656249 -4.411449918083245 4.998357391357422 -4.187652974057762 5.100364685058594-3.86655691142704 5.202371978759765 -3.456370989402685 5.304379272460937 -2.974261936074294 5.406386566162109 -2.443137155357121 5.508393859863281 -1.894504652441843 5.610401153564453 -1.367078174976005 5.712408447265624 -0.9023050100298249 5.814415740966797 -0.5323573575841695 5.916423034667968 -0.2692219366920132 6.01843032836914 -0.1047745876335641 6.120437622070312 -0.01593955616386777 6.222444915771484 0.02507844662681752 6.324452209472656 0.04088049050993046 6.426459503173827 0.04582596098146221 6.528466796875 0.04705941609406363 6.630474090576172 0.04729255605812091 6.732481384277343 0.0473236335498442 6.834488677978515 0.04732571430656037 6.936495971679687 0.04732516337288611 7.038503265380859 0.04732461243921186 would you please help me what must i do for obtaining the correct value according to another simulations? Regards, Mrs.Mahdavi On Thursday, January 1, 2015 6:14 PM, gromacs.org_gmx-users-requ...@maillist.sys.kth.se gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. Re: atom freezing (mah maz) 2. Re: atom freezing (Justin Lemkul) 3. Re: atom freezing (mah maz) 4. Re:
[gmx-users] Pulling
Dear Justin A. Lemkul, I want to use pulling code for calculate the PMF of a molecule at the across the DMPC, but i can't obtained a large pull across the membrane my pulling code was: ; Pull code pull= umbrella pull_geometry= position pull_dim= N N Y pull_start = yes; define initial COM distance 0 pull_ngroups= 1 pull_group0= DMPC pull_group1= QBH pull_k1= 1000 ; kJ mol^-1 nm^-2 pull_vec1= 0 0 0.5 after perl distances.pl step i obtained a summary.dat file. but in this file pulling was very low, just about 0.3nm. My molecule name is QBH and is out of membrane at bulk of the water and i want to pull it until center of bilayer. what must i do? -- 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] dangling bond error no matter what pdb file I use
Dear Justin A. Lemkul, I want to use pulling code for calculate the PMF of a molecule at the across the DMPC, but i can't obtained a large pull across the membrane my pulling code was: ; Pull code pull= umbrella pull_geometry= position pull_dim= N N Y pull_start = yes; define initial COM distance 0 pull_ngroups= 1 pull_group0= DMPC pull_group1= QBH pull_k1= 1000 ; kJ mol^-1 nm^-2 pull_vec1= 0 0 0.5 after perl distances.pl step i obtained a summary.dat file. but in this file pulling was very low, just about 0.3nm. My molecule name is QBH and is out of membrane at bulk of the water and i want to pull it until center of bilayer. what must i do? On Wednesday, November 5, 2014 1:26 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/4/14 4:38 PM, Thomas Lipscomb wrote: Dear Gromacs mailing list, I am at this step in a protein in membrane tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/01_pdb2gmx.html cd /home/tlipscomb/Desktop/Antimicrobial_Peptides/Gromacs/KALP /usr/local/gromacs/bin/gmx pdb2gmx -f 1SG0.pdb -o 1SG0_processed.gro -ignh -ter -water spc 13 2 2 13 is GROMOS96 53A6 2 means no terminus type I get this error, please help: --- Program gmx, VERSION 5.0.1 Source code file: /home/tlipscomb/gromacs-5.0.1/src/gromacs/gmxpreprocess/pdb2top.cpp, line: 1091 Fatal error: There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I know that 1SG0.pdb is correct because it worked for me on DOCK6 and it came from the PDB database. Is it the .tdb file messing up Gromacs? I just installed Gromacs and I thought that the .tdb file it came with is fine. This is what I have done so far with Gromacs: Installed Gromacs on linux cd /home/tlipscomb/Desktop/Antimicrobial_Peptides/Gromacs/KALP /usr/local/gromacs/bin/gmx pdb2gmx -f 1SG0.pdb -o 1SG0_processed.gro -ignh -ter -water spc 13 2 2 That's it. Once we resolve this bug I will go back to using model1.pdb (Maximin 3 peptide alpha helix) because that is the protein I need to simulate interacting with the membrane. This is the full command line stuff that happened: [tlipscomb@prime-radiant KALP]$ /usr/local/gromacs/bin/gmx pdb2gmx -f 1SG0.pdb -o 1SG0_processed.gro -ignh -ter -water spc GROMACS:gmx pdb2gmx, VERSION 5.0.1 GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar Aldert van Buuren Rudi van DrunenAnton Feenstra Sebastian Fritsch Gerrit GroenhofChristoph Junghans Peter Kasson Carsten Kutzner Per LarssonJustin A. Lemkul Magnus LundborgPieter Meulenhoff Erik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey ShvetsovMichael Shirts Alfons Sijbers Peter Tieleman Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2014, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx pdb2gmx, VERSION 5.0.1 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx pdb2gmx -f 1SG0.pdb -o 1SG0_processed.gro -ignh -ter -water spc Select the Force Field: From '/usr/local/gromacs/share/gromacs/top': 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003) 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995) 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996) 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000) 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006) 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) 7: AMBERGS force field (Garcia Sanbonmatsu, PNAS 99, 2782-2787, 2002) 8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins) 9: GROMOS96 43a1 force field 10: GROMOS96 43a2 force field (improved alkane dihedrals) 11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
[gmx-users] Pulling code
Dear Justin A. Lemkul, I want to use pulling code for calculate the PMF of a molecule at the across the DMPC, but i can't obtained a large pull across the membrane my pulling code was: ; Pull code pull= umbrella pull_geometry= position pull_dim= N N Y pull_start = yes; define initial COM distance 0 pull_ngroups= 1 pull_group0= DMPC pull_group1= QBH pull_k1= 1000 ; kJ mol^-1 nm^-2 pull_vec1= 0 0 0.5 after perl distances.pl step i obtained a summary.dat file. but in this file pulling was very low, just about 0.3nm. My molecule name is QBH and is out of membrane at bulk of the water and i want to pull it until center of bilayer. what must i do? Regards -- 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] Pulling code
Dear Justin A. Lemkul, I want to use pulling code for calculate the PMF of a molecule at the across the DMPC, but i can't obtained a large pull across the membrane my pulling code was: ; Pull code pull= umbrella pull_geometry= position pull_dim= N N Y pull_start = yes; define initial COM distance 0 pull_ngroups= 1 pull_group0= DMPC pull_group1= QBH pull_k1= 1000 ; kJ mol^-1 nm^-2 pull_vec1= 0 0 0.5 after perl distances.pl step i obtained a summary.dat file. but in this file pulling was very low, just about 0.3nm. My molecule name is QBH and is out of membrane at bulk of the water and i want to pull it until center of bilayer. what must i do? -- 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] Error
Dear Justin Lemkul, I want to know about kinds of lipid bilayers(POPC,DMPC,POPE,POPG,DOPC,DPPC) and their location in the nature,where are these lipids in human body?which kind of these lipid are for fungi? Many thanks, Mrs. Mahdavi On Wednesday, November 5, 2014 12:56 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/4/14 2:55 PM, asasa qsqs wrote: Dear Justin Lemkul, Is the position restrain very important for NVT and NPT steps? I have an ionic liquid that made of 2 fragment, cation and anion, but cation fragment didn't restrain at the NVT and NPT steps. I did production posre.itp for cation and anion .gro file and included to topology file but just anion was restrained,what must i do? The fact that you attempted to restrain a molecule and it was not restrained is a product of either (1) incorrect define keyword in the .mdp or (2) topology construction problem. If you want to restrain the molecule, you need to figure out which item failed. As to whether or not you need restraints, I'd say probably not in this case. For a small molecule that comprises part of the solution, restraints don't serve much of a purpose. For something larger, like a protein, restraints serve to avoid initial kicks from random velocities that may distort the structure. For a small molecule, the need for restraints is probably minimal. -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] Error
Is the position restrain very important for NVT and NPT steps? I have an ionic liquid that made of 2 fragment, cation and anion, but cation fragment didn't restrain at the NVT and NPT steps. I did production posre.itp for cation and anion .gro file and included to topology file but just anion was restrained,what must i do? Regards, Mahdavi -- 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] Error
Dear Justin Lemkul, Is the position restrain very important for NVT and NPT steps? I have an ionic liquid that made of 2 fragment, cation and anion, but cation fragment didn't restrain at the NVT and NPT steps. I did production posre.itp for cation and anion .gro file and included to topology file but just anion was restrained,what must i do? Regards, Mahdavi On Tuesday, November 4, 2014 6:02 PM, asasa qsqs sanaz_d...@yahoo.com wrote: Is the position restrain very important for NVT and NPT steps? I have an ionic liquid that made of 2 fragment, cation and anion, but cation fragment didn't restrain at the NVT and NPT steps. I did production posre.itp for cation and anion .gro file and included to topology file but just anion was restrained,what must i do? Regards, Mahdavi -- 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.
