Re: [gmx-users] rhombic dodecahedron construction
Hi Trayder, You can check the code of insane ( http://cgmartini.nl/cgmartini/index.php/insane), which sets up such a rhombic dodecahedron when -pbc optimal is given. Essentially, the routine boils down to: 1. Determining the diameter of the protein in the XY directions 2. Set the first vector u=(diam+pbcdistance, 0, 0) 3. Set the second vector v=(u/2, cos30*u, 0) 4. Set the third vector to w=(u/2, cos30*u/3, Z), where Z=(protZlength+pbcdistance) Changing the Z-dimension of the box (or the whole box) can be done manually (or using awk), changing the numbers of the last line in the gro file, which corresponds to (ux vy wz uy uz vx vz wx wy). Finally, note that the box (any box) is written in its triclinic representation, which is easiest to handle mathematically. Hope it helps, Tsjerk On Fri, May 23, 2014 at 4:42 AM, Trayder Thomas trayder.tho...@monash.eduwrote: Hi, I'm trying to figure out how to construct a rhombic dodecahedron for a membrane system. The manual (Section 3.2.1) states: There are two different orientations of a rhombic dodecahedron that satisfy equations 3.1, 3.2 and 3.3. The program editconf produces the orientation which has a square intersection with the xy-plane. This orientation was chosen because the first two box vectors coincide with the x and y-axis, which is easier to comprehend. The other orientation can be useful for simulations of membrane proteins. In this case the cross-section with the xy-plane is a hexagon, which has an area which is 14% smaller than the area of a square with the same image distance. The height of the box (cz) should be changed to obtain an optimal spacing. I can't figure out how to construct the system with a hexagon on the x-y plane, I presume I can rotate the box but I can only visualise the result as a triclinic cell. I also can't figure out how to adjust the height of the box, editconf only accepts a single magnitude for dodecahedron vector lengths. Any help would be greatly appreciated. Thanks in advance, -Trayder -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] how to generate .top file
Hi everyone.. I have a .pdb file with protein and gold slab .Problem is I can generate .top file for my protein with pdb2gmx but I want my slab in the same system .I can generate .gro file for both but what about .top file . Can any body help me with this issue .Thanks in advance. Regards Lovika -- 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 for reverse transformation
Dear Tsjerk, Thanks. I will definitely get in touch. Chandan On Thu, May 22, 2014 at 11:11 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Chandan, You may have to write a mapping file, as explained in one of the tutorials in the supplementary information of the paper. If that poses problems, you can contact me. I may be interested in adding new mappings :) Cheers, Tsjerk On May 22, 2014 6:42 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Tsjerk, Do the scripts available in the backward.zip file http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.ziphelp me to backmap a coarse-grained polymer? Chandan On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, I would argue that that method for reverse transformation is largely obsolete. Please have a look at http://www.cgmartini.nl/cgmartini/index.php/back Cheers, Tsjerk On Thu, May 22, 2014 at 4:26 PM, shivangi nangia shivangi.nan...@gmail.comwrote: Hello, I want to do a reverse transformation of my system containing: bi-layer, protein and water. The Martini website ( http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says to install gromacs version 3.3.1 I am currently using 4.6.1 gromacs version. ques A: Is this version incapable of the transformation? Also, the martini website says to: *1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that contains all necessary gromacs files for this exercise.* *2. Compile and/or source the modifi ed version of gromacs (remember this tool is based upon gromacs version 3.3.1 and needs the corresponding tricks and threats to be compiled.)* *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC* ques B:On performing untar on rev_trans.tar.gz there is no MARTINITUTORIAL directory ques C: On performing untar on gmx_rev.tar.gz there is no bin folder KIndly help. Thanks, sxn -- 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-usersor send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- 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 National Chemical Laboratory, 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. -- 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 National Chemical Laboratory, 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.
Re: [gmx-users] counter ions in coarse grained simulations
Hi Neha, You can simply add ions using genion. Its similar to what we do in AA system. You have to append #include martini_v2.0_ions.itp to your .top file. On Fri, May 23, 2014 at 6:17 AM, Neha Gandhi n.gandh...@gmail.com wrote: Hi List, My query is not really related to gromacs but I appreciate response from people who might have tried using coarse grained simualtions using Martini force field in gromacs. I haven't come across tutorial or mailing list where people have added counter ions to a coarse grained protein system. Do we also coarse grained counter-ions ? or Do I assume that some sort of potential will take care of the effect? Or are the parameters from atomistic force fields are retained for counter-ions? How do I add counter-ions in gromacs to coarse grained topology? Your feedback is appreciated. Regards, Neha -- 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. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- 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] how to generate .top file
for gold nano particle you can generate .top file using g_x2top, you have to make necessary changes in ffnonbonded.itp and atomname. n2t files. On Fri, May 23, 2014 at 3:09 PM, Lovika Moudgil lovikamoud...@gmail.comwrote: Hi everyone.. I have a .pdb file with protein and gold slab .Problem is I can generate .top file for my protein with pdb2gmx but I want my slab in the same system .I can generate .gro file for both but what about .top file . Can any body help me with this issue .Thanks in advance. Regards Lovika -- 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. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- 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] how to generate .top file
Hi Lovika, IIRC your gold is frozen, right? So you have a moleculetype definition for one gold atom (atomtype, mass, charge). You can just put it in the .top file after the #includes of the force field, like #include forcefield.itp #include protein.itp [ moleculetype ] AU 1 [ atoms ] 1 AU 1 UA UA 1 0196.96655 [ system ] Protein with gold [ molecules ] ... Hmm, I wonder, should one account for the gravitational effects of gold. Pretty heavy stuff :p Cheers, Tsjerk On Fri, May 23, 2014 at 11:39 AM, Lovika Moudgil lovikamoud...@gmail.comwrote: Hi everyone.. I have a .pdb file with protein and gold slab .Problem is I can generate .top file for my protein with pdb2gmx but I want my slab in the same system .I can generate .gro file for both but what about .top file . Can any body help me with this issue .Thanks in advance. Regards Lovika -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] how to generate .top file
Thanks for reply Abhijit... .I will definitely try this . Hey Tsjerk ... Is it possible , if I define all this in a different .itp and than define that .itp file in .top file ? On Fri, May 23, 2014 at 3:45 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lovika, IIRC your gold is frozen, right? So you have a moleculetype definition for one gold atom (atomtype, mass, charge). You can just put it in the .top file after the #includes of the force field, like #include forcefield.itp #include protein.itp [ moleculetype ] AU 1 [ atoms ] 1 AU 1 UA UA 1 0196.96655 [ system ] Protein with gold [ molecules ] ... Hmm, I wonder, should one account for the gravitational effects of gold. Pretty heavy stuff :p Cheers, Tsjerk On Fri, May 23, 2014 at 11:39 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi everyone.. I have a .pdb file with protein and gold slab .Problem is I can generate .top file for my protein with pdb2gmx but I want my slab in the same system .I can generate .gro file for both but what about .top file . Can any body help me with this issue .Thanks in advance. Regards Lovika -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] how to generate .top file
Thanks Tsjerk [?] Regards Lovika On Fri, May 23, 2014 at 4:17 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lovika, Yes, you can #include gold.itp or something along those lines. Cheers, Tsjerk On Fri, May 23, 2014 at 12:44 PM, Lovika Moudgil lovikamoud...@gmail.com wrote: Thanks for reply Abhijit... .I will definitely try this . Hey Tsjerk ... Is it possible , if I define all this in a different .itp and than define that .itp file in .top file ? On Fri, May 23, 2014 at 3:45 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lovika, IIRC your gold is frozen, right? So you have a moleculetype definition for one gold atom (atomtype, mass, charge). You can just put it in the .top file after the #includes of the force field, like #include forcefield.itp #include protein.itp [ moleculetype ] AU 1 [ atoms ] 1 AU 1 UA UA 1 0196.96655 [ system ] Protein with gold [ molecules ] ... Hmm, I wonder, should one account for the gravitational effects of gold. Pretty heavy stuff :p Cheers, Tsjerk On Fri, May 23, 2014 at 11:39 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi everyone.. I have a .pdb file with protein and gold slab .Problem is I can generate .top file for my protein with pdb2gmx but I want my slab in the same system .I can generate .gro file for both but what about .top file . Can any body help me with this issue .Thanks in advance. Regards Lovika -- 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-usersor send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] how to generate .top file
Hi Lovika, Yes, you can #include gold.itp or something along those lines. Cheers, Tsjerk On Fri, May 23, 2014 at 12:44 PM, Lovika Moudgil lovikamoud...@gmail.comwrote: Thanks for reply Abhijit... .I will definitely try this . Hey Tsjerk ... Is it possible , if I define all this in a different .itp and than define that .itp file in .top file ? On Fri, May 23, 2014 at 3:45 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Lovika, IIRC your gold is frozen, right? So you have a moleculetype definition for one gold atom (atomtype, mass, charge). You can just put it in the .top file after the #includes of the force field, like #include forcefield.itp #include protein.itp [ moleculetype ] AU 1 [ atoms ] 1 AU 1 UA UA 1 0196.96655 [ system ] Protein with gold [ molecules ] ... Hmm, I wonder, should one account for the gravitational effects of gold. Pretty heavy stuff :p Cheers, Tsjerk On Fri, May 23, 2014 at 11:39 AM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi everyone.. I have a .pdb file with protein and gold slab .Problem is I can generate .top file for my protein with pdb2gmx but I want my slab in the same system .I can generate .gro file for both but what about .top file . Can any body help me with this issue .Thanks in advance. Regards Lovika -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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. -- Tsjerk A. Wassenaar, Ph.D. -- 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] RDF of solvation shell molecules
On 5/23/14, 12:37 AM, sujithkakkat . wrote: Hello Chandan, Thank you for the response. I have used g_rdf, but I guess it gives the RDF for the whole system. Say, if I choose water oxygen, it will plot RDF from water molecules in the whole system. But, I want the RDF for the solvation shell water molecules ,leaving the bulk water . I came across such a plot in an article where the author studied the structure of solvation shell . So do you think it is possible to do that GROMACS? You already have it. The first solvation shell is the first peak in the RDF. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
Re: [gmx-users] Query regarding dssp plot
Thanks a lot Justin. It worked :) On Wed, May 21, 2014 at 5:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 5/21/14, 8:13 AM, Aditya Padhi wrote: Dear Justin, Thank you for the reply. I was using my 50 ns trajectory for generating the .xpm and .eps files. But when I tried the first 200 ps trajectory, I can see a clear image with helical content. I was wondering how to solve this because I have to use the whole 50 ns .tpr and .trr files. Please suggest me. I already did: The list does not accept attachments. If you want to supply an image, upload it to a file-sharing server. If the image is simply distorted, that's where .m2p files are useful to alter the size properties of the matrix. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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. -- Aditya Kumar Padhi Ph.D Scholar School of Biological Sciences (SBS) Indian Institute of Technology Delhi New Delhi-110016, India Contact no:+91-9711539958 -- 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] md-vv run with the Nose-Hoover thermostat crashed..
Hello gmx-users, I tried to run a simulation to calculate a specific heat capacity of infinite molecular crystal with the md-vv integrator and Nose-Hoover thermostat on ver 4.6, but it crashed immediately with only the message of Segmentation fault. Does anyone have a similar experience or any good ideas for this problems? I would appreciate very much if somebody gives any comments on this matter. Thank you, Yu Yu OGAWA, PhD Cermav-CNRS, Grenoble, France -- 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] md-vv run with the Nose-Hoover thermostat crashed..
First, find something out. Does the installation work for any other simulation? What does the log file say? Have you equilibrated your system first? Does another integrator or thermostat work? Mark On Fri, May 23, 2014 at 3:54 PM, Yu Ogawa ayo...@gmail.com wrote: Hello gmx-users, I tried to run a simulation to calculate a specific heat capacity of infinite molecular crystal with the md-vv integrator and Nose-Hoover thermostat on ver 4.6, but it crashed immediately with only the message of Segmentation fault. Does anyone have a similar experience or any good ideas for this problems? I would appreciate very much if somebody gives any comments on this matter. Thank you, Yu Yu OGAWA, PhD Cermav-CNRS, Grenoble, France -- 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] md-vv run with the Nose-Hoover thermostat crashed..
Dear Mark, At the very last part of the log file I can find outputs at 0.0 ps, but nothing more below. Have you equilibrated your system first? Does another integrator or thermostat work? Yes, my mdrun program works with the other inputs, and I think the initial structure is equilibrated enough because I can run a NPT simulation properly with this structure file with md integrator and berendsen thermostat. I also tried the similar calculation with md integrator and Nose-Hoover. In this case I could start running the simulation, but the temperature was not controlled, and it stayed around the value of gen_temp. Thank you, Yu 2014-05-23 16:33 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: First, find something out. Does the installation work for any other simulation? What does the log file say? Have you equilibrated your system first? Does another integrator or thermostat work? Mark On Fri, May 23, 2014 at 3:54 PM, Yu Ogawa ayo...@gmail.com wrote: Hello gmx-users, I tried to run a simulation to calculate a specific heat capacity of infinite molecular crystal with the md-vv integrator and Nose-Hoover thermostat on ver 4.6, but it crashed immediately with only the message of Segmentation fault. Does anyone have a similar experience or any good ideas for this problems? I would appreciate very much if somebody gives any comments on this matter. Thank you, Yu Yu OGAWA, PhD Cermav-CNRS, Grenoble, France -- 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. -- 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 for reverse transformation
Dear Tsjerk, My system contains CG (Martini): POPC bilayer, 21 AA peptide, water and ions. I realize that for all-atom the topology file should not contain details for water and ions. As a test while trying to understand and get familiarized with backward. As of now I am trying to convert CG peptide only to all-atom. I am using the following command: ./initram.sh -f protein.gro -p topol.top -from martini -po backmapped.top -to gromos54a7 (I obtained the topol.top file for the peptide by using: pdb2gmx -f peptide.pdb -o peptide.gro -p, selecting ff charmm and TIP3P water) The script is giving me the following error: Traceback (most recent call last): File /shared/maylab/shivi/fhv/inverse_cg/try1/backward.py, line 644, in ? struc = Structure(options[-f].value,strict=options[-strict].value) File /shared/maylab/shivi/fhv/inverse_cg/try1/backward.py, line 388, in __init__ if not all(chain): NameError: global name 'all' is not defined Could you please help. Thanks, sxn On Fri, May 23, 2014 at 6:03 AM, Chandan Choudhury iitd...@gmail.comwrote: Dear Tsjerk, Thanks. I will definitely get in touch. Chandan On Thu, May 22, 2014 at 11:11 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Chandan, You may have to write a mapping file, as explained in one of the tutorials in the supplementary information of the paper. If that poses problems, you can contact me. I may be interested in adding new mappings :) Cheers, Tsjerk On May 22, 2014 6:42 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Tsjerk, Do the scripts available in the backward.zip file http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.ziphelp me to backmap a coarse-grained polymer? Chandan On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, I would argue that that method for reverse transformation is largely obsolete. Please have a look at http://www.cgmartini.nl/cgmartini/index.php/back Cheers, Tsjerk On Thu, May 22, 2014 at 4:26 PM, shivangi nangia shivangi.nan...@gmail.comwrote: Hello, I want to do a reverse transformation of my system containing: bi-layer, protein and water. The Martini website ( http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation) says to install gromacs version 3.3.1 I am currently using 4.6.1 gromacs version. ques A: Is this version incapable of the transformation? Also, the martini website says to: *1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that contains all necessary gromacs files for this exercise.* *2. Compile and/or source the modifi ed version of gromacs (remember this tool is based upon gromacs version 3.3.1 and needs the corresponding tricks and threats to be compiled.)* *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC* ques B:On performing untar on rev_trans.tar.gz there is no MARTINITUTORIAL directory ques C: On performing untar on gmx_rev.tar.gz there is no bin folder KIndly help. Thanks, sxn -- 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-usersor send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- 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-usersor send a mail to gmx-users-requ...@gromacs.org. -- -- Chandan Kumar Choudhury National Chemical Laboratory, 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. -- 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] genion
dear users i studied on amyloid beta peptide with zinc cation and i choosed 1ze9 as my pdb file can i assume Zn without charge in protein simulation alone, or i have to using the amyloid beta peptide alone as pdb for instance,1iyt??? best wishes -- 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] Question regarding gromacs error of g_membed
Hello all. I am a brand new user of Gromacs, and I am not even sure I am sending this email to the appropriate people. If my email goes to the wrong people, I apologize in advance I am trying to create a pdb (or gro) structure which containts protein and membrane, DPPC to be exact. After following a certain path, I have managed to create all necessary files, and now I am about to use command g_membed. So, I use g_membed as follows g_membed -f membed.tpr -p system.top -xyinit 0.1 -xyend 1.0 -nxy 1000 -o memtraj.trr Gromacs gives me a message, saying that it has created a .dat file, and that now I need to run mdrun in a specific way. So I call mdun as follows mdrun -s membed.tpr -membed membed.dat -o memtraj.trr -c membedded.gro -e ener.edr -nt 1 -cpt -1 -mp system.top Gromacs then interactively asks me to choose Select a group to embed in the membrane: and I choose 1, protein Then it asks me to choose Select a group to embed Protein into (e.g. the membrane): and I choose 13, DPPC After that, it looks like mdrun crushes, and it gives me the following error: --- Program mdrun, VERSION 4.6.5 Source code file: /home/$$$/PROGRAMS/GROMACS/gromacs-4.6.5/src/gmxlib/mtop_util.c, line: 215 Software inconsistency error: gmx_mtop_atomlookup_settle_init called without settles For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I have no idea how to address this error. Can someone tell me what my mistake may probably be? I kind of found the source code online, but still I am not familiar (yet) with the variables. If you can forward this email to the appropriate people, I would greatly appreciate it. Thanks S. -- 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] md-vv run with the Nose-Hoover thermostat crashed..
What has gen_temp to do with it? You sound like you're doing an equilibration, then generating velocities at gen_temp, then running with a thermostat with a different ref_t from gen_temp. Why? Mark On Fri, May 23, 2014 at 5:01 PM, Yu Ogawa ayo...@gmail.com wrote: Dear Mark, At the very last part of the log file I can find outputs at 0.0 ps, but nothing more below. Have you equilibrated your system first? Does another integrator or thermostat work? Yes, my mdrun program works with the other inputs, and I think the initial structure is equilibrated enough because I can run a NPT simulation properly with this structure file with md integrator and berendsen thermostat. I also tried the similar calculation with md integrator and Nose-Hoover. In this case I could start running the simulation, but the temperature was not controlled, and it stayed around the value of gen_temp. Thank you, Yu 2014-05-23 16:33 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: First, find something out. Does the installation work for any other simulation? What does the log file say? Have you equilibrated your system first? Does another integrator or thermostat work? Mark On Fri, May 23, 2014 at 3:54 PM, Yu Ogawa ayo...@gmail.com wrote: Hello gmx-users, I tried to run a simulation to calculate a specific heat capacity of infinite molecular crystal with the md-vv integrator and Nose-Hoover thermostat on ver 4.6, but it crashed immediately with only the message of Segmentation fault. Does anyone have a similar experience or any good ideas for this problems? I would appreciate very much if somebody gives any comments on this matter. Thank you, Yu Yu OGAWA, PhD Cermav-CNRS, Grenoble, France -- 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. -- 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] md-vv run with the Nose-Hoover thermostat crashed..
Sorry for my poor explanation. I tried to simulate a temperature rising process from 0 K to 500 K. At first I did a simulation with gen_vel=no, and the temperature was just around 3 to 5 K and never rose up. then I tried to give a velocities with gen_temp though I don't know if it's correct or not. 2014-05-23 18:42 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: What has gen_temp to do with it? You sound like you're doing an equilibration, then generating velocities at gen_temp, then running with a thermostat with a different ref_t from gen_temp. Why? Mark On Fri, May 23, 2014 at 5:01 PM, Yu Ogawa ayo...@gmail.com wrote: Dear Mark, At the very last part of the log file I can find outputs at 0.0 ps, but nothing more below. Have you equilibrated your system first? Does another integrator or thermostat work? Yes, my mdrun program works with the other inputs, and I think the initial structure is equilibrated enough because I can run a NPT simulation properly with this structure file with md integrator and berendsen thermostat. I also tried the similar calculation with md integrator and Nose-Hoover. In this case I could start running the simulation, but the temperature was not controlled, and it stayed around the value of gen_temp. Thank you, Yu 2014-05-23 16:33 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: First, find something out. Does the installation work for any other simulation? What does the log file say? Have you equilibrated your system first? Does another integrator or thermostat work? Mark On Fri, May 23, 2014 at 3:54 PM, Yu Ogawa ayo...@gmail.com wrote: Hello gmx-users, I tried to run a simulation to calculate a specific heat capacity of infinite molecular crystal with the md-vv integrator and Nose-Hoover thermostat on ver 4.6, but it crashed immediately with only the message of Segmentation fault. Does anyone have a similar experience or any good ideas for this problems? I would appreciate very much if somebody gives any comments on this matter. Thank you, Yu Yu OGAWA, PhD Cermav-CNRS, Grenoble, France -- 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-usersor 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. -- 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. -- 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] md-vv run with the Nose-Hoover thermostat crashed..
On 5/23/14, 1:02 PM, Yu Ogawa wrote: Sorry for my poor explanation. I tried to simulate a temperature rising process from 0 K to 500 K. At first I did a simulation with gen_vel=no, and the temperature was just around 3 to 5 K and never rose up. then I tried to give a velocities with gen_temp though I don't know if it's correct or not. You'll need to post complete .mdp files of whatever it is you're doing. Trying to provide help based on fragmented information is very hard, and it could be a simple matter of some incorrect settings, but we can't tell. -Justin 2014-05-23 18:42 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: What has gen_temp to do with it? You sound like you're doing an equilibration, then generating velocities at gen_temp, then running with a thermostat with a different ref_t from gen_temp. Why? Mark On Fri, May 23, 2014 at 5:01 PM, Yu Ogawa ayo...@gmail.com wrote: Dear Mark, At the very last part of the log file I can find outputs at 0.0 ps, but nothing more below. Have you equilibrated your system first? Does another integrator or thermostat work? Yes, my mdrun program works with the other inputs, and I think the initial structure is equilibrated enough because I can run a NPT simulation properly with this structure file with md integrator and berendsen thermostat. I also tried the similar calculation with md integrator and Nose-Hoover. In this case I could start running the simulation, but the temperature was not controlled, and it stayed around the value of gen_temp. Thank you, Yu 2014-05-23 16:33 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: First, find something out. Does the installation work for any other simulation? What does the log file say? Have you equilibrated your system first? Does another integrator or thermostat work? Mark On Fri, May 23, 2014 at 3:54 PM, Yu Ogawa ayo...@gmail.com wrote: Hello gmx-users, I tried to run a simulation to calculate a specific heat capacity of infinite molecular crystal with the md-vv integrator and Nose-Hoover thermostat on ver 4.6, but it crashed immediately with only the message of Segmentation fault. Does anyone have a similar experience or any good ideas for this problems? I would appreciate very much if somebody gives any comments on this matter. Thank you, Yu Yu OGAWA, PhD Cermav-CNRS, Grenoble, France -- 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-usersor 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. -- 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. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
Re: [gmx-users] md-vv run with the Nose-Hoover thermostat crashed..
This is my mdp file. ;define = -DFLEX_SPC constraints = none ;constraint_algorithm = LINCS integrator = md dt = 0.0005 ;ps ! nsteps = 1 ; total 50 ns. nstcomm = 2 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy = 1 nstlist = 5 ns_type = grid coulombtype = PME rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = nose-hoover tau_t = 0.1 tc-grps= GLC ref_t = 5 annealing = single annealing_npoints = 109 annealing_time = 0 200 800 1000 1600 ... 41200 41800 42000 42600 42800 annealing_temp = 5 20 20 40 40 ... 40 40 20 20 0 Pcoupl = MTTK tau_p = 0.1 pcoupltype = anisotropic compressibility = 1e-5 1e-5 1e-7 1e-5 1e-5 1e-5 ref_p = 1.0 1.0 1.0 0 0 0 gen_vel = yes gen_temp = 5 gen_seed= 173529 pbc = xyz periodic_molecules = yes DispCorr= EnerPres optimize_fft= yes 2014-05-23 19:07 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 5/23/14, 1:02 PM, Yu Ogawa wrote: Sorry for my poor explanation. I tried to simulate a temperature rising process from 0 K to 500 K. At first I did a simulation with gen_vel=no, and the temperature was just around 3 to 5 K and never rose up. then I tried to give a velocities with gen_temp though I don't know if it's correct or not. You'll need to post complete .mdp files of whatever it is you're doing. Trying to provide help based on fragmented information is very hard, and it could be a simple matter of some incorrect settings, but we can't tell. -Justin 2014-05-23 18:42 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: What has gen_temp to do with it? You sound like you're doing an equilibration, then generating velocities at gen_temp, then running with a thermostat with a different ref_t from gen_temp. Why? Mark On Fri, May 23, 2014 at 5:01 PM, Yu Ogawa ayo...@gmail.com wrote: Dear Mark, At the very last part of the log file I can find outputs at 0.0 ps, but nothing more below. Have you equilibrated your system first? Does another integrator or thermostat work? Yes, my mdrun program works with the other inputs, and I think the initial structure is equilibrated enough because I can run a NPT simulation properly with this structure file with md integrator and berendsen thermostat. I also tried the similar calculation with md integrator and Nose-Hoover. In this case I could start running the simulation, but the temperature was not controlled, and it stayed around the value of gen_temp. Thank you, Yu 2014-05-23 16:33 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: First, find something out. Does the installation work for any other simulation? What does the log file say? Have you equilibrated your system first? Does another integrator or thermostat work? Mark On Fri, May 23, 2014 at 3:54 PM, Yu Ogawa ayo...@gmail.com wrote: Hello gmx-users, I tried to run a simulation to calculate a specific heat capacity of infinite molecular crystal with the md-vv integrator and Nose-Hoover thermostat on ver 4.6, but it crashed immediately with only the message of Segmentation fault. Does anyone have a similar experience or any good ideas for this problems? I would appreciate very much if somebody gives any comments on this matter. Thank you, Yu Yu OGAWA, PhD Cermav-CNRS, Grenoble, France -- 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-usersor 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. -- 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
Re: [gmx-users] md-vv run with the Nose-Hoover thermostat crashed..
On 5/23/14, 1:26 PM, Yu Ogawa wrote: This is my mdp file. ;define = -DFLEX_SPC constraints = none ;constraint_algorithm = LINCS integrator = md dt = 0.0005 ;ps ! nsteps = 1 ; total 50 ns. nstcomm = 2 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy = 1 nstlist = 5 ns_type = grid coulombtype = PME rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = nose-hoover tau_t = 0.1 tc-grps= GLC ref_t = 5 annealing = single annealing_npoints = 109 annealing_time = 0 200 800 1000 1600 ... 41200 41800 42000 42600 42800 annealing_temp = 5 20 20 40 40 ... 40 40 20 20 0 Pcoupl = MTTK tau_p = 0.1 pcoupltype = anisotropic compressibility = 1e-5 1e-5 1e-7 1e-5 1e-5 1e-5 ref_p = 1.0 1.0 1.0 0 0 0 gen_vel = yes gen_temp = 5 gen_seed= 173529 pbc = xyz periodic_molecules = yes DispCorr= EnerPres optimize_fft= yes Generating new velocities with Nose-Hoover can be very unstable; grompp should have thrown a warning about this. You should equilibrate for a while at the starting temperature, then pass the .cpt file from the equilibration to the annealing run to preserve the previous ensemble. Re-generating velocities negates any equilibration done previously, and whether or not the simulation works is, at that point, a bit of a coin-flip. -Justin 2014-05-23 19:07 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 5/23/14, 1:02 PM, Yu Ogawa wrote: Sorry for my poor explanation. I tried to simulate a temperature rising process from 0 K to 500 K. At first I did a simulation with gen_vel=no, and the temperature was just around 3 to 5 K and never rose up. then I tried to give a velocities with gen_temp though I don't know if it's correct or not. You'll need to post complete .mdp files of whatever it is you're doing. Trying to provide help based on fragmented information is very hard, and it could be a simple matter of some incorrect settings, but we can't tell. -Justin 2014-05-23 18:42 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: What has gen_temp to do with it? You sound like you're doing an equilibration, then generating velocities at gen_temp, then running with a thermostat with a different ref_t from gen_temp. Why? Mark On Fri, May 23, 2014 at 5:01 PM, Yu Ogawa ayo...@gmail.com wrote: Dear Mark, At the very last part of the log file I can find outputs at 0.0 ps, but nothing more below. Have you equilibrated your system first? Does another integrator or thermostat work? Yes, my mdrun program works with the other inputs, and I think the initial structure is equilibrated enough because I can run a NPT simulation properly with this structure file with md integrator and berendsen thermostat. I also tried the similar calculation with md integrator and Nose-Hoover. In this case I could start running the simulation, but the temperature was not controlled, and it stayed around the value of gen_temp. Thank you, Yu 2014-05-23 16:33 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: First, find something out. Does the installation work for any other simulation? What does the log file say? Have you equilibrated your system first? Does another integrator or thermostat work? Mark On Fri, May 23, 2014 at 3:54 PM, Yu Ogawa ayo...@gmail.com wrote: Hello gmx-users, I tried to run a simulation to calculate a specific heat capacity of infinite molecular crystal with the md-vv integrator and Nose-Hoover thermostat on ver 4.6, but it crashed immediately with only the message of Segmentation fault. Does anyone have a similar experience or any good ideas for this problems? I would appreciate very much if somebody gives any comments on this matter. Thank you, Yu Yu OGAWA, PhD Cermav-CNRS, Grenoble, France -- 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-usersor 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. -- Gromacs Users mailing list * Please search the archive at
Re: [gmx-users] Gromacs for reverse transformation
Hi sxn, It means your python version is outdated. The function 'all' was introduced in version 2.5. Better upgrade to 2.7. If you really can't I can maybe write a workaround. Cheers, Tsjerk On May 23, 2014 5:31 PM, shivangi nangia shivangi.nan...@gmail.com wrote: Dear Tsjerk, My system contains CG (Martini): POPC bilayer, 21 AA peptide, water and ions. I realize that for all-atom the topology file should not contain details for water and ions. As a test while trying to understand and get familiarized with backward. As of now I am trying to convert CG peptide only to all-atom. I am using the following command: ./initram.sh -f protein.gro -p topol.top -from martini -po backmapped.top -to gromos54a7 (I obtained the topol.top file for the peptide by using: pdb2gmx -f peptide.pdb -o peptide.gro -p, selecting ff charmm and TIP3P water) The script is giving me the following error: Traceback (most recent call last): File /shared/maylab/shivi/fhv/inverse_cg/try1/backward.py, line 644, in ? struc = Structure(options[-f].value,strict=options[-strict].value) File /shared/maylab/shivi/fhv/inverse_cg/try1/backward.py, line 388, in __init__ if not all(chain): NameError: global name 'all' is not defined Could you please help. Thanks, sxn On Fri, May 23, 2014 at 6:03 AM, Chandan Choudhury iitd...@gmail.com wrote: Dear Tsjerk, Thanks. I will definitely get in touch. Chandan On Thu, May 22, 2014 at 11:11 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Chandan, You may have to write a mapping file, as explained in one of the tutorials in the supplementary information of the paper. If that poses problems, you can contact me. I may be interested in adding new mappings :) Cheers, Tsjerk On May 22, 2014 6:42 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Tsjerk, Do the scripts available in the backward.zip file http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.ziphelp me to backmap a coarse-grained polymer? Chandan On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, I would argue that that method for reverse transformation is largely obsolete. Please have a look at http://www.cgmartini.nl/cgmartini/index.php/back Cheers, Tsjerk On Thu, May 22, 2014 at 4:26 PM, shivangi nangia shivangi.nan...@gmail.comwrote: Hello, I want to do a reverse transformation of my system containing: bi-layer, protein and water. The Martini website ( http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation ) says to install gromacs version 3.3.1 I am currently using 4.6.1 gromacs version. ques A: Is this version incapable of the transformation? Also, the martini website says to: *1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that contains all necessary gromacs files for this exercise.* *2. Compile and/or source the modifi ed version of gromacs (remember this tool is based upon gromacs version 3.3.1 and needs the corresponding tricks and threats to be compiled.)* *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC* ques B:On performing untar on rev_trans.tar.gz there is no MARTINITUTORIAL directory ques C: On performing untar on gmx_rev.tar.gz there is no bin folder KIndly help. Thanks, sxn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore 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-usersor send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- 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-usersor send a mail to gmx-users-requ...@gromacs.org. -- -- Chandan Kumar Choudhury National Chemical Laboratory, 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
[gmx-users] PBC problems??
My protein breaks according to viewing the traj in VMD and graphing the RMSD of the protein C-terminus I have tried all combinations of trjconv -pbc -center -box center and nothing works..I was able to get online and find a tutorial that says trjconv -pbc mol, should stop the problem, but this failedIsn't there a way for the protein and water to be wrapped or COM calculations done DURING MD to remove translation, rotation so that post-MD modification of trajectories is unnecessary??...If I make an index group of the N-terminus of the protein this problems goes away or if I use the whole protein...It is only when I attempt to get the rms of the C-terminus region that I get this graphing problem (traj plots look like Histograms)Not sure what this means since if I observe the trajectories in VMD the whole protein breaks up Thanks, Steve -- 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 for reverse transformation
Hi Tsjerk, Thanks so much for the reply. I updated to python version 3.3.2 and I tried to run the backward.py using python3 backward.py I get the following error: File backward.py, line 351 try: ^ TabError: inconsistent use of tabs and spaces in indentation May be its a minor thing to fix but I am not familiar with Python. Thanks, sxn On Fri, May 23, 2014 at 2:09 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, It means your python version is outdated. The function 'all' was introduced in version 2.5. Better upgrade to 2.7. If you really can't I can maybe write a workaround. Cheers, Tsjerk On May 23, 2014 5:31 PM, shivangi nangia shivangi.nan...@gmail.com wrote: Dear Tsjerk, My system contains CG (Martini): POPC bilayer, 21 AA peptide, water and ions. I realize that for all-atom the topology file should not contain details for water and ions. As a test while trying to understand and get familiarized with backward. As of now I am trying to convert CG peptide only to all-atom. I am using the following command: ./initram.sh -f protein.gro -p topol.top -from martini -po backmapped.top -to gromos54a7 (I obtained the topol.top file for the peptide by using: pdb2gmx -f peptide.pdb -o peptide.gro -p, selecting ff charmm and TIP3P water) The script is giving me the following error: Traceback (most recent call last): File /shared/maylab/shivi/fhv/inverse_cg/try1/backward.py, line 644, in ? struc = Structure(options[-f].value,strict=options[-strict].value) File /shared/maylab/shivi/fhv/inverse_cg/try1/backward.py, line 388, in __init__ if not all(chain): NameError: global name 'all' is not defined Could you please help. Thanks, sxn On Fri, May 23, 2014 at 6:03 AM, Chandan Choudhury iitd...@gmail.com wrote: Dear Tsjerk, Thanks. I will definitely get in touch. Chandan On Thu, May 22, 2014 at 11:11 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Chandan, You may have to write a mapping file, as explained in one of the tutorials in the supplementary information of the paper. If that poses problems, you can contact me. I may be interested in adding new mappings :) Cheers, Tsjerk On May 22, 2014 6:42 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Tsjerk, Do the scripts available in the backward.zip file http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.ziphelp me to backmap a coarse-grained polymer? Chandan On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, I would argue that that method for reverse transformation is largely obsolete. Please have a look at http://www.cgmartini.nl/cgmartini/index.php/back Cheers, Tsjerk On Thu, May 22, 2014 at 4:26 PM, shivangi nangia shivangi.nan...@gmail.comwrote: Hello, I want to do a reverse transformation of my system containing: bi-layer, protein and water. The Martini website ( http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation ) says to install gromacs version 3.3.1 I am currently using 4.6.1 gromacs version. ques A: Is this version incapable of the transformation? Also, the martini website says to: *1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that contains all necessary gromacs files for this exercise.* *2. Compile and/or source the modifi ed version of gromacs (remember this tool is based upon gromacs version 3.3.1 and needs the corresponding tricks and threats to be compiled.)* *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC* ques B:On performing untar on rev_trans.tar.gz there is no MARTINITUTORIAL directory ques C: On performing untar on gmx_rev.tar.gz there is no bin folder KIndly help. Thanks, sxn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore 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-usersor send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore posting! * Can't post? Read
Re: [gmx-users] md-vv run with the Nose-Hoover thermostat crashed..
Dear Justin, Thank you very much for your advice. Okay, I will try according to your procedure. Yu 2014-05-23 19:48 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 5/23/14, 1:26 PM, Yu Ogawa wrote: This is my mdp file. ;define = -DFLEX_SPC constraints = none ;constraint_algorithm = LINCS integrator = md dt = 0.0005 ;ps ! nsteps = 1 ; total 50 ns. nstcomm = 2 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy = 1 nstlist = 5 ns_type = grid coulombtype = PME rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = nose-hoover tau_t = 0.1 tc-grps= GLC ref_t = 5 annealing = single annealing_npoints = 109 annealing_time = 0 200 800 1000 1600 ... 41200 41800 42000 42600 42800 annealing_temp = 5 20 20 40 40 ... 40 40 20 20 0 Pcoupl = MTTK tau_p = 0.1 pcoupltype = anisotropic compressibility = 1e-5 1e-5 1e-7 1e-5 1e-5 1e-5 ref_p = 1.0 1.0 1.0 0 0 0 gen_vel = yes gen_temp = 5 gen_seed= 173529 pbc = xyz periodic_molecules = yes DispCorr= EnerPres optimize_fft= yes Generating new velocities with Nose-Hoover can be very unstable; grompp should have thrown a warning about this. You should equilibrate for a while at the starting temperature, then pass the .cpt file from the equilibration to the annealing run to preserve the previous ensemble. Re-generating velocities negates any equilibration done previously, and whether or not the simulation works is, at that point, a bit of a coin-flip. -Justin 2014-05-23 19:07 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 5/23/14, 1:02 PM, Yu Ogawa wrote: Sorry for my poor explanation. I tried to simulate a temperature rising process from 0 K to 500 K. At first I did a simulation with gen_vel=no, and the temperature was just around 3 to 5 K and never rose up. then I tried to give a velocities with gen_temp though I don't know if it's correct or not. You'll need to post complete .mdp files of whatever it is you're doing. Trying to provide help based on fragmented information is very hard, and it could be a simple matter of some incorrect settings, but we can't tell. -Justin 2014-05-23 18:42 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: What has gen_temp to do with it? You sound like you're doing an equilibration, then generating velocities at gen_temp, then running with a thermostat with a different ref_t from gen_temp. Why? Mark On Fri, May 23, 2014 at 5:01 PM, Yu Ogawa ayo...@gmail.com wrote: Dear Mark, At the very last part of the log file I can find outputs at 0.0 ps, but nothing more below. Have you equilibrated your system first? Does another integrator or thermostat work? Yes, my mdrun program works with the other inputs, and I think the initial structure is equilibrated enough because I can run a NPT simulation properly with this structure file with md integrator and berendsen thermostat. I also tried the similar calculation with md integrator and Nose-Hoover. In this case I could start running the simulation, but the temperature was not controlled, and it stayed around the value of gen_temp. Thank you, Yu 2014-05-23 16:33 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: First, find something out. Does the installation work for any other simulation? What does the log file say? Have you equilibrated your system first? Does another integrator or thermostat work? Mark On Fri, May 23, 2014 at 3:54 PM, Yu Ogawa ayo...@gmail.com wrote: Hello gmx-users, I tried to run a simulation to calculate a specific heat capacity of infinite molecular crystal with the md-vv integrator and Nose-Hoover thermostat on ver 4.6, but it crashed immediately with only the message of Segmentation fault. Does anyone have a similar experience or any good ideas for this problems? I would appreciate very much if somebody gives any comments on this matter. Thank you, Yu Yu OGAWA, PhD Cermav-CNRS, Grenoble, France -- 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-usersor 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?
Re: [gmx-users] Gromacs for reverse transformation
Hi sxn, Now that's rather unfortunate! Python 3.x has distinct differences in syntax. If you can (also) install 2.7. Otherwise, maybe it's time I adapt the program for python 3... :p Cheers, Tsjerk On May 23, 2014 9:25 PM, shivangi nangia shivangi.nan...@gmail.com wrote: Hi Tsjerk, Thanks so much for the reply. I updated to python version 3.3.2 and I tried to run the backward.py using python3 backward.py I get the following error: File backward.py, line 351 try: ^ TabError: inconsistent use of tabs and spaces in indentation May be its a minor thing to fix but I am not familiar with Python. Thanks, sxn On Fri, May 23, 2014 at 2:09 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, It means your python version is outdated. The function 'all' was introduced in version 2.5. Better upgrade to 2.7. If you really can't I can maybe write a workaround. Cheers, Tsjerk On May 23, 2014 5:31 PM, shivangi nangia shivangi.nan...@gmail.com wrote: Dear Tsjerk, My system contains CG (Martini): POPC bilayer, 21 AA peptide, water and ions. I realize that for all-atom the topology file should not contain details for water and ions. As a test while trying to understand and get familiarized with backward. As of now I am trying to convert CG peptide only to all-atom. I am using the following command: ./initram.sh -f protein.gro -p topol.top -from martini -po backmapped.top -to gromos54a7 (I obtained the topol.top file for the peptide by using: pdb2gmx -f peptide.pdb -o peptide.gro -p, selecting ff charmm and TIP3P water) The script is giving me the following error: Traceback (most recent call last): File /shared/maylab/shivi/fhv/inverse_cg/try1/backward.py, line 644, in ? struc = Structure(options[-f].value,strict=options[-strict].value) File /shared/maylab/shivi/fhv/inverse_cg/try1/backward.py, line 388, in __init__ if not all(chain): NameError: global name 'all' is not defined Could you please help. Thanks, sxn On Fri, May 23, 2014 at 6:03 AM, Chandan Choudhury iitd...@gmail.com wrote: Dear Tsjerk, Thanks. I will definitely get in touch. Chandan On Thu, May 22, 2014 at 11:11 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Chandan, You may have to write a mapping file, as explained in one of the tutorials in the supplementary information of the paper. If that poses problems, you can contact me. I may be interested in adding new mappings :) Cheers, Tsjerk On May 22, 2014 6:42 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Tsjerk, Do the scripts available in the backward.zip file http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.ziphelp me to backmap a coarse-grained polymer? Chandan On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, I would argue that that method for reverse transformation is largely obsolete. Please have a look at http://www.cgmartini.nl/cgmartini/index.php/back Cheers, Tsjerk On Thu, May 22, 2014 at 4:26 PM, shivangi nangia shivangi.nan...@gmail.comwrote: Hello, I want to do a reverse transformation of my system containing: bi-layer, protein and water. The Martini website ( http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation ) says to install gromacs version 3.3.1 I am currently using 4.6.1 gromacs version. ques A: Is this version incapable of the transformation? Also, the martini website says to: *1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that contains all necessary gromacs files for this exercise.* *2. Compile and/or source the modifi ed version of gromacs (remember this tool is based upon gromacs version 3.3.1 and needs the corresponding tricks and threats to be compiled.)* *source /where-ever-you-installed-it/gromacs-3.3.1/bin/GMXRC* ques B:On performing untar on rev_trans.tar.gz there is no MARTINITUTORIAL directory ques C: On performing untar on gmx_rev.tar.gz there is no bin folder KIndly help. Thanks, sxn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_Listbefore posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] md-vv run with the Nose-Hoover thermostat crashed..
I might just add: Your time-scale for controlling your thermostat (tau_t) is set equal to your timescale time-scale for controlling your barostat (tau_p). Having these two relaxation times set equal can be quite unstable, especially if your system is not already in equilibrium. You typically want your tau_p to be larger (how much varies but ~ a factor of 10 is safe) than your tau_t. This is because you want the thermal degrees of freedom to be well equilibrated much faster than the system box changes size. The value of time constants that produce stable simulations also depends on your system. A couple of good rules of thumb for tau_t and tau_p would be: 1. Choose tau_t than the intermolecular collision time of your system. (This can be determined from a calculation of the velocity autocorrelation function). 2. Choose tau_p so that it is larger than the sound transit time of your system.. i.e. make tau_p larger than the time needed by a sound wave to travel across your system. This is because the fluctuations in density caused by changing the simulation box size need to dissipate and correlate throughout the system and they do so at ~ the speed of sound. I hope this helps. Thermo/Barostating can be really frustrating and cause a lot of headaches if your time-scales aren't right! -Thomas On Fri, May 23, 2014 at 3:10 PM, Yu Ogawa ayo...@gmail.com wrote: Dear Justin, Thank you very much for your advice. Okay, I will try according to your procedure. Yu 2014-05-23 19:48 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 5/23/14, 1:26 PM, Yu Ogawa wrote: This is my mdp file. ;define = -DFLEX_SPC constraints = none ;constraint_algorithm = LINCS integrator = md dt = 0.0005 ;ps ! nsteps = 1 ; total 50 ns. nstcomm = 2 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy = 1 nstlist = 5 ns_type = grid coulombtype = PME rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = nose-hoover tau_t = 0.1 tc-grps= GLC ref_t = 5 annealing = single annealing_npoints = 109 annealing_time = 0 200 800 1000 1600 ... 41200 41800 42000 42600 42800 annealing_temp = 5 20 20 40 40 ... 40 40 20 20 0 Pcoupl = MTTK tau_p = 0.1 pcoupltype = anisotropic compressibility = 1e-5 1e-5 1e-7 1e-5 1e-5 1e-5 ref_p = 1.0 1.0 1.0 0 0 0 gen_vel = yes gen_temp = 5 gen_seed= 173529 pbc = xyz periodic_molecules = yes DispCorr= EnerPres optimize_fft= yes Generating new velocities with Nose-Hoover can be very unstable; grompp should have thrown a warning about this. You should equilibrate for a while at the starting temperature, then pass the .cpt file from the equilibration to the annealing run to preserve the previous ensemble. Re-generating velocities negates any equilibration done previously, and whether or not the simulation works is, at that point, a bit of a coin-flip. -Justin 2014-05-23 19:07 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 5/23/14, 1:02 PM, Yu Ogawa wrote: Sorry for my poor explanation. I tried to simulate a temperature rising process from 0 K to 500 K. At first I did a simulation with gen_vel=no, and the temperature was just around 3 to 5 K and never rose up. then I tried to give a velocities with gen_temp though I don't know if it's correct or not. You'll need to post complete .mdp files of whatever it is you're doing. Trying to provide help based on fragmented information is very hard, and it could be a simple matter of some incorrect settings, but we can't tell. -Justin 2014-05-23 18:42 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: What has gen_temp to do with it? You sound like you're doing an equilibration, then generating velocities at gen_temp, then running with a thermostat with a different ref_t from gen_temp. Why? Mark On Fri, May 23, 2014 at 5:01 PM, Yu Ogawa ayo...@gmail.com wrote: Dear Mark, At the very last part of the log file I can find outputs at 0.0 ps, but nothing more below. Have you equilibrated your system first? Does another integrator or thermostat work? Yes, my mdrun program works with the other inputs, and I think the initial structure is equilibrated enough because I can run a NPT simulation properly with this structure file with md integrator and berendsen thermostat. I also tried the similar calculation with md integrator and Nose-Hoover. In this case
Re: [gmx-users] PBC problems??
On 5/23/14, 2:51 PM, Steve Seibold wrote: My protein breaks according to viewing the traj in VMD and graphing the RMSD of the protein C-terminus I have tried all combinations of trjconv -pbc -center -box center and nothing works..I was able to get online and find a tutorial that says trjconv -pbc mol, should stop the problem, but this failedIsn't there a way for the protein and water to be wrapped or COM calculations done DURING MD to remove translation, rotation so that post-MD modification of trajectories is unnecessary??...If I make an index group of the The integration doesn't need to follow our visualization convenience, so there's no reason to sacrifice performance to re-wrap coordinates on the fly. N-terminus of the protein this problems goes away or if I use the whole protein...It is only when I attempt to get the rms of the C-terminus region that I get this graphing problem (traj plots look like Histograms)Not sure what this means since if I observe the trajectories in VMD the whole protein breaks up Centering a single protein within a box should be very easy using any of the options you have posted. trjconv -pbc mol -ur compact -center should be all that's necessary for a simple system like this. Are you sure the box is large enough to accommodate the protein? If it keeps breaking in spite of trjconv, that might suggest your box is not suitable, such that re-imaging can't fix things. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 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.
Re: [gmx-users] Gromacs for reverse transformation
Hi Tsjerk, Thanks so much for all the help. I tried both 2.6.5 and 2.7 versions both on running python on backward.py give the following error: Traceback (most recent call last): File backward.py, line 644, in module struc = Structure(options[-f].value,strict=options[-strict].value) File backward.py, line 318, in __init__ self.atoms = [pdbAtom(i,strict) for i in lines if isPDBAtom(i) or rest.append(i)] TypeError: 'NoneType' object is not iterable sxn On Fri, May 23, 2014 at 3:37 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, Now that's rather unfortunate! Python 3.x has distinct differences in syntax. If you can (also) install 2.7. Otherwise, maybe it's time I adapt the program for python 3... :p Cheers, Tsjerk On May 23, 2014 9:25 PM, shivangi nangia shivangi.nan...@gmail.com wrote: Hi Tsjerk, Thanks so much for the reply. I updated to python version 3.3.2 and I tried to run the backward.py using python3 backward.py I get the following error: File backward.py, line 351 try: ^ TabError: inconsistent use of tabs and spaces in indentation May be its a minor thing to fix but I am not familiar with Python. Thanks, sxn On Fri, May 23, 2014 at 2:09 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, It means your python version is outdated. The function 'all' was introduced in version 2.5. Better upgrade to 2.7. If you really can't I can maybe write a workaround. Cheers, Tsjerk On May 23, 2014 5:31 PM, shivangi nangia shivangi.nan...@gmail.com wrote: Dear Tsjerk, My system contains CG (Martini): POPC bilayer, 21 AA peptide, water and ions. I realize that for all-atom the topology file should not contain details for water and ions. As a test while trying to understand and get familiarized with backward. As of now I am trying to convert CG peptide only to all-atom. I am using the following command: ./initram.sh -f protein.gro -p topol.top -from martini -po backmapped.top -to gromos54a7 (I obtained the topol.top file for the peptide by using: pdb2gmx -f peptide.pdb -o peptide.gro -p, selecting ff charmm and TIP3P water) The script is giving me the following error: Traceback (most recent call last): File /shared/maylab/shivi/fhv/inverse_cg/try1/backward.py, line 644, in ? struc = Structure(options[-f].value,strict=options[-strict].value) File /shared/maylab/shivi/fhv/inverse_cg/try1/backward.py, line 388, in __init__ if not all(chain): NameError: global name 'all' is not defined Could you please help. Thanks, sxn On Fri, May 23, 2014 at 6:03 AM, Chandan Choudhury iitd...@gmail.com wrote: Dear Tsjerk, Thanks. I will definitely get in touch. Chandan On Thu, May 22, 2014 at 11:11 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Chandan, You may have to write a mapping file, as explained in one of the tutorials in the supplementary information of the paper. If that poses problems, you can contact me. I may be interested in adding new mappings :) Cheers, Tsjerk On May 22, 2014 6:42 PM, Chandan Choudhury iitd...@gmail.com wrote: Hi Tsjerk, Do the scripts available in the backward.zip file http://www.cgmartini.nl/cgmartini/images/tools/backward/backward.ziphelp me to backmap a coarse-grained polymer? Chandan On Thu, May 22, 2014 at 8:31 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi sxn, I would argue that that method for reverse transformation is largely obsolete. Please have a look at http://www.cgmartini.nl/cgmartini/index.php/back Cheers, Tsjerk On Thu, May 22, 2014 at 4:26 PM, shivangi nangia shivangi.nan...@gmail.comwrote: Hello, I want to do a reverse transformation of my system containing: bi-layer, protein and water. The Martini website ( http://md.chem.rug.nl/cgmartini/index.php/reverse-transformation ) says to install gromacs version 3.3.1 I am currently using 4.6.1 gromacs version. ques A: Is this version incapable of the transformation? Also, the martini website says to: *1. Unpack the rev_trans.tar.gz in the MARTINITUTORIAL directory that contains all necessary gromacs files for this exercise.* *2. Compile and/or source the modifi ed version of gromacs (remember this
Re: [gmx-users] md-vv run with the Nose-Hoover thermostat crashed..
To say nothing of the fact that the manual clearly states MTTK is not useable with the md integrator. But who reads manuals these days? :-) Mark On Fri, May 23, 2014 at 9:49 PM, Thomas C. O'Connor tocon...@jhu.eduwrote: I might just add: Your time-scale for controlling your thermostat (tau_t) is set equal to your timescale time-scale for controlling your barostat (tau_p). Having these two relaxation times set equal can be quite unstable, especially if your system is not already in equilibrium. You typically want your tau_p to be larger (how much varies but ~ a factor of 10 is safe) than your tau_t. This is because you want the thermal degrees of freedom to be well equilibrated much faster than the system box changes size. The value of time constants that produce stable simulations also depends on your system. A couple of good rules of thumb for tau_t and tau_p would be: 1. Choose tau_t than the intermolecular collision time of your system. (This can be determined from a calculation of the velocity autocorrelation function). 2. Choose tau_p so that it is larger than the sound transit time of your system.. i.e. make tau_p larger than the time needed by a sound wave to travel across your system. This is because the fluctuations in density caused by changing the simulation box size need to dissipate and correlate throughout the system and they do so at ~ the speed of sound. I hope this helps. Thermo/Barostating can be really frustrating and cause a lot of headaches if your time-scales aren't right! -Thomas On Fri, May 23, 2014 at 3:10 PM, Yu Ogawa ayo...@gmail.com wrote: Dear Justin, Thank you very much for your advice. Okay, I will try according to your procedure. Yu 2014-05-23 19:48 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 5/23/14, 1:26 PM, Yu Ogawa wrote: This is my mdp file. ;define = -DFLEX_SPC constraints = none ;constraint_algorithm = LINCS integrator = md dt = 0.0005 ;ps ! nsteps = 1 ; total 50 ns. nstcomm = 2 nstxout = 1 nstvout = 1 nstfout = 0 nstlog = 1 nstenergy = 1 nstlist = 5 ns_type = grid coulombtype = PME rlist = 0.9 rcoulomb= 0.9 rvdw= 0.9 ; Berendsen temperature coupling is on in two groups Tcoupl = nose-hoover tau_t = 0.1 tc-grps= GLC ref_t = 5 annealing = single annealing_npoints = 109 annealing_time = 0 200 800 1000 1600 ... 41200 41800 42000 42600 42800 annealing_temp = 5 20 20 40 40 ... 40 40 20 20 0 Pcoupl = MTTK tau_p = 0.1 pcoupltype = anisotropic compressibility = 1e-5 1e-5 1e-7 1e-5 1e-5 1e-5 ref_p = 1.0 1.0 1.0 0 0 0 gen_vel = yes gen_temp = 5 gen_seed= 173529 pbc = xyz periodic_molecules = yes DispCorr= EnerPres optimize_fft= yes Generating new velocities with Nose-Hoover can be very unstable; grompp should have thrown a warning about this. You should equilibrate for a while at the starting temperature, then pass the .cpt file from the equilibration to the annealing run to preserve the previous ensemble. Re-generating velocities negates any equilibration done previously, and whether or not the simulation works is, at that point, a bit of a coin-flip. -Justin 2014-05-23 19:07 GMT+02:00 Justin Lemkul jalem...@vt.edu: On 5/23/14, 1:02 PM, Yu Ogawa wrote: Sorry for my poor explanation. I tried to simulate a temperature rising process from 0 K to 500 K. At first I did a simulation with gen_vel=no, and the temperature was just around 3 to 5 K and never rose up. then I tried to give a velocities with gen_temp though I don't know if it's correct or not. You'll need to post complete .mdp files of whatever it is you're doing. Trying to provide help based on fragmented information is very hard, and it could be a simple matter of some incorrect settings, but we can't tell. -Justin 2014-05-23 18:42 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: What has gen_temp to do with it? You sound like you're doing an equilibration, then generating velocities at gen_temp, then running with a thermostat with a different ref_t from gen_temp. Why? Mark On Fri, May 23, 2014 at 5:01 PM, Yu Ogawa ayo...@gmail.com wrote: Dear Mark, At the very last part of the log file I can find outputs at 0.0 ps, but nothing more below. Have you equilibrated your system first? Does another
[gmx-users] large free energy difference of mutating ATP to GTP in solution using FEP method in Gromacs-4.6.5
Dear all, I want to calculate the free energy difference of mutating ATP to GTP in solution using FEP method. Firstly, the hybrid topology and structure files for A (ATP) and B (GTP) state using dummy atoms were constructed. Secondly, the system is running for 10 ns to reach an equilibrium state. And then the structure at 10 ns is as the starting structure to carry out FEP calculation. In the course of FEP, the coulomb interaction was firstly changed, and then the VDW interactions. Total 32 lambda points are set in the mdp file shown in the following: integrator = sd nsteps = 10 dt = 0.002 nstenergy= 1000 nstlog = 5000 nstcalcenergy= 100 nstcomm = 1 cutoff-scheme= group rlist= 1.2 dispcorr = EnerPres vdw-type = switch ;cut-off lengths rvdw = 1.1 rvdw-switch = 1 ; Coulomb interactions coulombtype = pme rcoulomb = 1.2 fourierspacing = 0.12 ; Constraints constraints = all-bonds ; set temperature to 310K tcoupl = v-rescale tc-grps = system tau-t= 1.0 ref-t= 310 ; pressure control pcoupl = Parrinello-Rahman ref-p= 1 compressibility= 4.5e-5 tau-p= 0.5 ; and set the free energy parameters free-energy = yes sc-power = 1 sc-sigma = 0.3 sc-alpha = 0.5 sc-coul = no sc-r-power = 6 ; we still want the molecule to interact with itself at lambda=0 couple-intramol = no couple-lambda0 = vdw-q couple-lambda1 = vdw-q ; $LAMBDA$ changed from 0 to 32 init-lambda-state= $LAMBDA$ nstdhdl = 100 calc-lambda-neighbors= 1 fep-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.01 0.03 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 ;change electrostatic and then LJ interaction coul-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.00 1.00 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0 vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.01 0.03 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0 atom part of hybrid topology file is : [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB 1 O3 1RAGO1G 1 -0.95260 16.00 2 P 1RAG PG 21.26500 31.00 3 O3 1RAGO2G 3 -0.95260 16.00 4 O3 1RAGO3G 4 -0.95260 16.00 5 OS 1RAGO3B 5 -0.53220 16.00 6 P 1RAG PB 61.38520 31.00 7 O2 1RAGO1B 7 -0.88940 16.00 8 O2 1RAGO2B 8 -0.88940 16.00 9 OS 1RAGO3A 9 -0.56890 16.00 10 P 1RAG PA 101.25320 31.00 11 O2 1RAGO1A 11 -0.87990 16.00 12 O2 1RAGO2A 12 -0.87990 16.00 13 OS 1RAGO5* 13 -0.59870 16.00 14 CT 1RAGC5* 140.05580 12.00 15 H1 1RAGH50 150.06790 1.008000 16 H1 1RAGH51 160.06790 1.008000 17 CT 1RAGC4* 170.10650 12.00 18 H1 1RAGH40 180.11740 1.008000 19 OS 1RAGO4* 19 -0.35480 16.00 20 CT 1RAGC1* 200.03940 12.00 CT 0.01910 12.00 21 H2 1RAGH10 210.20070 1.008000 H2 0.20060 1.008000 22 N* 1RAG N9 22 -0.02510 14.00 N* 0.04920 14.00 23 CK 1RAG C8 230.20060 12.00 CK 0.13740 12.00 24 H5 1RAGH80 240.15530 1.008000 H5 0.16400 1.008000 25 NB 1RAG N7 25 -0.60730 14.00 NB -0.57090 14.00 26 CB 1RAG C5 260.05150 12.00 CB 0.17440 12.00 27 CA 1RAG C6 270.70090 12.00C 0.47700 12.00 28 N2 1RAG N6 28 -0.90190 14.00O -0.55970 16.00 29 H 1RAGH60 290.41150 1.008000 DUM_1 0.00 1.0080 30 H 1RAGH61 300.41150 1.008000
