[gmx-users] error in grompp command
hello gromacs i an working on protein ligand complex with lipid membrane (popc) grompp -f minim.mdp -c popc128.gro -p topol_popc.top -o em.tpr -maxwarn -1 after this fatal error atomtypes CA not found and only md.oonly mdout is formed kindly help -- 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] Changed order of molecules in top
Hi, I have a problem with that the order of atoms in my topology does not match the order of atoms in the gro-file. I use amber99sb and I have built itp-files on my own for the molecules that are not present in the library. Each IMI contains 9 atoms and each SOL 3 atoms and the ZN is one atom so in total it should be 9*2+3*2+1=25 atoms in total, which is present in the .gro file, but when I run with the topology-file pasted below I get a error the this file contains 34 atoms. This is my topologyfile: ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Additional atom types [ atomtypes ] ; name at_name at_num mass charge ptype sigmaepsilon ; sw ref Zn++ Zn++30 65.37000 2.000A1.94216e-01 1.046 ; 1 Stote Proteins 23:12 1995 ; Include topology for ions #include zn.itp ; Include water topology #include spcetestamber.itp ; Include topology for imidazole #include imiamberrtp.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [system ] ; Name ZnHis2Wa2 [ molecules ] ; Compound#mols ZN2+ 1 IMI 2 SOL 2 - Fatal error: number of coordinates in coordinate file (ZnHis2Wa2optM06.gro, 25) does not match topology (ZnHis2Wa2optM06amber.top, 34) Since the difference is 9 atoms, I thought that the difference is one IMI, so I tried with one less IMI in the topology, printed below. ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Additional atom types [ atomtypes ] ; name at_name at_num mass charge ptype sigmaepsilon ; sw ref Zn++ Zn++30 65.37000 2.000A1.94216e-01 1.046 ; 1 Stote Proteins 23:12 1995 ; Include topology for ions #include zn.itp ; Include water topology #include spcetestamber.itp ; Include topology for imidazole #include imiamberrtp.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [system ] ; Name ZnHis2Wa2 [ molecules ] ; Compound#mols ZN2+ 1 IMI 1 SOL 2 Then the number of atoms matches, but I get the information that the atom names does not match. Warning: atom name 1 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro does not match (C1 - ZN) Warning: atom name 2 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro does not match (N1 - C1) By this message it gets clear to me that the topology makes an IMI first and then go on to the ZN and then probably the IMI and the two waters specified in the top-file. Why does it do that? And how do I correct it? Thanks in advance for help. -- Emma Ahlstrand PhD student Linnaeus University Faculty of Health and Life Sciences 391 82 Kalmar / 351 95 Växjö +46 480 446 152 Telephone +46 73 905 7186 Mobile emma.ahlstr...@lnu.se http://lnu.se/ccbg -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error in grompp command
Hi Rinu, See what forcefield files you include in your topology, then go to the force field folders and check if those indeed have that atom types. You must indeed be missing the CA type. Likely, you just forgot to include some topology file. V On 2 Jul 2014, at 10:23, gromacs.org_gmx-users-requ...@maillist.sys.kth.semailto:gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: -- Message: 2 Date: Wed, 2 Jul 2014 12:26:07 +0530 From: RINU KHATTRI nickname.mi...@gmail.commailto:nickname.mi...@gmail.com To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Subject: [gmx-users] error in grompp command Message-ID: caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.commailto:caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 hello gromacs i an working on protein ligand complex with lipid membrane (popc) grompp -f minim.mdp -c popc128.gro -p topol_popc.top -o em.tpr -maxwarn -1 after this fatal error atomtypes CA not found and only md.oonly mdout is formed kindly help -- -- 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] Some basic questions about trajconv
Hi, trjconv is a very versatile tool. if you do trjconv -h it will tell you: Option -center centers the system in the box. The user can select the group which is used to determine the geometrical center. Option -boxcenter sets the location of the center of the box for options -pbc and -center. The center options are: tric: half of the sum of the box vectors, rect: half of the box diagonal, zero: zero. Use option -pbc mol in addition to -center when you want all molecules in the box after the centering. I think you need to use command -center in conjunction with -pbc. For -center select your group of atoms and for the whole trjconv you will need to select no-water option. You have to play around to see what will give you necessary result. You possibly would need to iterate the trjconv over: 1st remove water, then centre atoms. V On 2 Jul 2014, at 10:23, gromacs.org_gmx-users-requ...@maillist.sys.kth.semailto:gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: -- Message: 1 Date: Wed, 2 Jul 2014 12:52:32 +0800 From: Yip Yew Mun yipy0...@gmail.commailto:yipy0...@gmail.com To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Subject: [gmx-users] Some basic questions about trajconv Message-ID: 0e0d56b7-c31a-4170-8ef3-a879f29fd...@gmail.commailto:0e0d56b7-c31a-4170-8ef3-a879f29fd...@gmail.com Content-Type: text/plain; charset=windows-1252 Hi all, I?ve recently switched from AMBER and started using Gromacs. I have just ran a CG MD and I wish to do post-analysis on the trajectory. So if I wish to center my molecule in the water box, then remove the waters, what should the appropriate command for trajconv be? Thanks, any help would be greatly appreciated. =) Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry Biological Chemistry School of Physical Mathematical Sciences | Nanyang Technological University | Singapore 639798 Tel: (+65) 97967803 | Email: yipy0...@e.ntu.edu.sgmailto:yipy0...@e.ntu.edu.sg | GMT+8h -- 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] restart the calculation----- checksum error
Hello dear gmx-users, I tried to restart the calculation, but there is always one checksum error as: Program mdrun_mpi, VERSION 4.6.1 Source code file: /home/kit/ipc/nw2011/gromacs-4.6.1/src/gmxlib/checkpoint.c, line: 2155 Fatal error: Checksum wrong for 'pull.xvg'. The file has been replaced or its contents have been modified. Cannot do appending because of this condition. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors But I did nothing to this pull.xvg file.. I ever did this restarting before, and I found if I didn't output the (xx).xvg file, the restarting calculation works. So one solution maybe that I redo the calcuation without outputting the pull.xvg filebut it will takes quite a long time again... Anybody has some suggestions? Thank you so much! Best Yanan -- 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] obtaining .gro timeframe
On 7/1/14, 11:28 PM, Chetan Mahajan wrote: Thanks, Justin. *Until now, I was thinking that xtc coordinates are wrapped. It's good to know that coordinates from xtc files are unwrapped (please comment if not correct, since we talked only with respect to gro That is correct. mdrun doesn't care about our visualization convenience. No sense in wasting performance doing imaging on the fly when it's not necessary. file). *But I am confused at another thing. I have known at the origin of the box is at one of its vertices ( is that not true?). *Then why are some coordinates in .gro file (the one generated at the end of gromacs MD run) negative, if coordinates are wrapped in the box?* Molecules are made whole; sometimes they're translated in the positive direction, sometimes in the negative direction, depending on how the molecule is being reconstructed. Is my original command using trjconv okay? OK is relative. In this case, you seem troubled by the slight difference in convention, but there's nothing wrong with the command. If you want trjconv to make molecules whole, use -pbc mol or -pbc whole. Your original command simply dumps the coordinates and does nothing about periodicity. Whereas I do get a sample x-coordinate in .gro file, generated at the end of MD run (let's call it gro1) from that in .gro file, generated using trjconv on xtc (let's call it gro2) by adding a box length to concerned coordinate in gro2, (as shown in excerpt 1) , it's only by subtracting a boxlength that we interconvert between similar values, as shown in excerpt 2 of the SAME file. *Why is there no consistency of conversion between SAME two .gro files for all the coordinates? How do I mathematically obtain file 2 from file 1 with some consistent measure? * See above. trjconv will do it for you. -Justin - : for .gro file at the end of gromacs MD run (gro1) + : for .gro timeframe file obtained from .xtc trajectory ( using trjconv) (gro2) *EXCERT 1* - 11SOLHW1 2188 3.244 3.071 10.934 - 11SOLHW2 2189 3.211 2.940 10.842 + 11SOLHW1 2188 0.023 3.071 10.934 + 11SOLHW2 2189 -0.011 2.940 10.842 *EXCERT 2* - 56SOLHW1 2323 -0.031 1.076 1.130 - 56SOLHW2 2324 -0.040 1.096 1.292 + 56SOLHW1 2323 3.191 1.076 1.130 + 56SOLHW2 2324 3.182 1.096 1.292 Thanks Chetan On Tue, Jul 1, 2014 at 8:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/1/14, 9:08 PM, Chetan Mahajan wrote: Thanks, Justin. Are you saying, the coordinates in .gro file extracted from xtc trajectory are not wrapped, whereas those in the .gro file generated at the end of gromacs MD run are wrapped in the box? Yes, unless you've manipulated the trajectory in some way with trjconv beforehand. Now I have a question: the negative coordinates that are present in the following text are from .gro file (generated at the end of MD run), whereas positive ones are from .gro file obtained using trjconv on xtc. Either way, it's a periodicity effect. Molecules are made whole. -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. -- == 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] Inserting required no. of water using genbox -ci -nmol crashing
On 7/2/14, 12:02 AM, shivangi nangia wrote: Hello gmx-users, This is regarding inserting required number of TIP3P water molecules using genbox. I have a system containing POPC, peptide, water molecules ions. For some system set up, I had to delete all the waters and ions ( The box size was not changed). Now I want to insert the same number of water molecules back into the box (35228) but the job keeps crashing. When I run it interactively it says there is not enough memory and if I submit in queue the job just exits or goes into zombie mode. System size: 9.38943 9.38943 15.54950 command: genbox_mpi -cp popc_pep.gro -ci spc.gro -nmol 35228 -o solvated.gro I have tried varied kinds of spc.gro containing just one water molecule, 2 ,3 and 4 (system size fixed accordingly using editconf -d 0 ) On using -cs option, lesser number of water molecules get inserted than 35228 on using the spc216.gro found in the /apps/gromacs/top folder. That means there's not enough room in the box for that many waters in those given configurations. You run out of memory because (1) using -ci -nmol is a horribly inefficient way to insert waters and (2) genbox simply can't find enough space, so it keeps going until system resources are exhausted. -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] TOP file conversion
On 7/2/14, 12:27 AM, Andy Chao wrote: Dear GROMACS Users: I would like to convert a GRO file to the TOP file. Is it a better way to use pdb2gmx -f device.gro -p device.top or to use g_x2top -f device.gro -ff oplsaa -o device.top? That depends. If the contents of device.gro consist of a linear polymer of definable units in the .rtp file, pdb2gmx is the way to go. If it is non-linear or you don't have suitable .rtp entries, g_x2top may be better. In theory, you can accomplish an equivalent result with either, but without more detail of what's going on, there's no real solid recommendation to make. -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] error in grompp command
On 7/2/14, 6:07 AM, RINU KHATTRI wrote: hello gromacs users i used 43a1 force field(Gromacs 4.5.7) in the atomtype.atp file in the place of CA CA2+ is present in ffnonbonded.itp file CA and CA2+ both are present according to tutorial i have been followed all the step still em.tpr not formed atomtype CA not found CA is the gmx.ff nomenclature for the calcium type, so that suggests you're mixing and matching force fields (note that gmx.ff has been removed from the latest Gromacs version, since it should not be used). Without explicit detail of your topology (i.e. post your files so they can be downloaded), there's very little that can be done to suggest where things have gone wrong. I strongly suspect you've mixed and matched force fields somewhere, which is easy to do when dealing with complex systems. Pick a force field, stick to it exactly. -Justin On Wed, Jul 2, 2014 at 3:19 PM, ERASTOVA V. valentina.erast...@durham.ac.uk wrote: Hi Rinu, See what forcefield files you include in your topology, then go to the force field folders and check if those indeed have that atom types. You must indeed be missing the CA type. Likely, you just forgot to include some topology file. V On 2 Jul 2014, at 10:23, gromacs.org_gmx-users-requ...@maillist.sys.kth.se mailto:gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: -- Message: 2 Date: Wed, 2 Jul 2014 12:26:07 +0530 From: RINU KHATTRI nickname.mi...@gmail.commailto: nickname.mi...@gmail.com To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Subject: [gmx-users] error in grompp command Message-ID: caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.com mailto:caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 hello gromacs i an working on protein ligand complex with lipid membrane (popc) grompp -f minim.mdp -c popc128.gro -p topol_popc.top -o em.tpr -maxwarn -1 after this fatal error atomtypes CA not found and only md.oonly mdout is formed kindly help -- -- 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] restart the calculation----- checksum error
On 7/2/14, 5:59 AM, Guo, Yanan (IPC) wrote: Hello dear gmx-users, I tried to restart the calculation, but there is always one checksum error as: Program mdrun_mpi, VERSION 4.6.1 Source code file: /home/kit/ipc/nw2011/gromacs-4.6.1/src/gmxlib/checkpoint.c, line: 2155 Fatal error: Checksum wrong for 'pull.xvg'. The file has been replaced or its contents have been modified. Cannot do appending because of this condition. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors But I did nothing to this pull.xvg file.. I ever did this restarting before, and I found if I didn't output the (xx).xvg file, the restarting calculation works. So one solution maybe that I redo the calcuation without outputting the pull.xvg filebut it will takes quite a long time again... Anybody has some suggestions? Tell mdrun not to append, and just concatenate the files later. -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] Changed order of molecules in top
On 7/2/14, 3:31 AM, Emma Ahlstrand wrote: Hi, I have a problem with that the order of atoms in my topology does not match the order of atoms in the gro-file. I use amber99sb and I have built itp-files on my own for the molecules that are not present in the library. Each IMI contains 9 atoms and each SOL 3 atoms and the ZN is one atom so in total it should be 9*2+3*2+1=25 atoms in total, which is present in the .gro file, but when I run with the topology-file pasted below I get a error the this file contains 34 atoms. This is my topologyfile: ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Additional atom types [ atomtypes ] ; name at_name at_num mass charge ptype sigmaepsilon ; sw ref Zn++ Zn++30 65.37000 2.000A1.94216e-01 1.046 ; 1 Stote Proteins 23:12 1995 ; Include topology for ions #include zn.itp ; Include water topology #include spcetestamber.itp ; Include topology for imidazole #include imiamberrtp.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [system ] ; Name ZnHis2Wa2 [ molecules ] ; Compound#mols ZN2+ 1 IMI 2 SOL 2 - Fatal error: number of coordinates in coordinate file (ZnHis2Wa2optM06.gro, 25) does not match topology (ZnHis2Wa2optM06amber.top, 34) Since the difference is 9 atoms, I thought that the difference is one IMI, so I tried with one less IMI in the topology, printed below. ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Additional atom types [ atomtypes ] ; name at_name at_num mass charge ptype sigmaepsilon ; sw ref Zn++ Zn++30 65.37000 2.000A1.94216e-01 1.046 ; 1 Stote Proteins 23:12 1995 ; Include topology for ions #include zn.itp ; Include water topology #include spcetestamber.itp ; Include topology for imidazole #include imiamberrtp.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [system ] ; Name ZnHis2Wa2 [ molecules ] ; Compound#mols ZN2+ 1 IMI 1 SOL 2 Then the number of atoms matches, but I get the information that the atom names does not match. Warning: atom name 1 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro does not match (C1 - ZN) Warning: atom name 2 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro does not match (N1 - C1) By this message it gets clear to me that the topology makes an IMI first and then go on to the ZN and then probably the IMI and the two waters specified in the top-file. Why does it do that? And how do I correct it? No, your coordinate file has IMI first. grompp expects the input coordinates and topology to be in the same order. You list Zn, IMI, and SOL in the .top - that is the expected order in the coordinates. As reported by grompp, that is not the case. There should be no probably here; with such a small system it should be very easy to inspect the .gro file in a text editor and see precisely what is going on. -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.
[gmx-users] Use trjconv in parallel,
Hello, in short : it is possible ? I use the gromacs v4.6.5. Thanks Stéphane -- 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] Use trjconv in parallel,
On 02 Jul 2014, at 12:55, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello, in short : it is possible ? I use the gromacs v4.6.5. No. Carsten Thanks Stéphane -- 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] grompp does not find atomtype
On 7/2/14, 4:40 AM, Dawid das wrote: I have managed to deal with this problem in following way: In topology file some bonding parameters were actually missing but some bonding parameters were not needed, e.g. U-B or dihedral parameters for atoms which are not connected, that is they belong to different parts of my new residue. I found parameters for the missing ones and hashed (;) them out. Is it what I can do? Like I say, theses bonding parameters that I hashed out were for atom types which are not connected directly. Then I performed minimization with steepest descent and in output file I got: 4655e+05 Fmax= 6.53501e+03, atom= 1003^MStep= 426, Dmax= 2.5e-06 nm, Epot= -4.54655e+05 Fmax= 9.45125e+03, atom= 1003^MStep= 427, Dmax= 1.2e-06 nm, Epot= -4.54655e+05 Fmax= 1.25724e+04, atom= 1003^M Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 428 steps, but did not reach the requested Fmax 1000. Potential Energy = -4.5465475e+05 Maximum force = 1.7057922e+04 on atom 1003 Norm of force = 1.1677969e+02 But I continued with NVT MD simulation. This is my nvt-md.mdp file: title = NVT MD integrator = md constraints = all-bonds dt = 0.001 nsteps = 2 nstenergy = 100 nstlist = 10 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 100 nstxtcout = 1000 xtcprecision= 500 ns_type = grid coulombtype = PME rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 These cutoffs are incorrect for using CHARMM force fields. See previous posts on proper settings. tcoupl = nose-hoover tc-grps = Protein SOL NA tau_t = 0.1 0.1 0.1 ;(3 numbers - because 3 tc-grps) ref_t = 100 100 100 ;(3 numbers - because 3 tc-grps) Coupling water and ions separately is not sensible. http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do Pcoupl = No gen_vel = yes gen_temp= 100 gen_seed= 173529 energygrps = Protein SOL NA constraint_algorithm = LINCS pbc = xyz And in my NVT output I got error for LINCS: relative constraint deviation after LINCS: rms 0.036755, max 1.509884 (between atoms 998 and 1000) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1001 1003 62.10.1410 0.2032 0.1410 1001 1002 68.10.1240 0.1962 0.1240 1000 1001 88.10.1460 0.3276 0.1460 998 1000 90.00.1390 0.3489 0.1390 986 1000 90.70.1400 0.2237 0.1400 985986 30.70.1300 0.1499 0.1300 Wrote pdb files with previous and current coordinates These atoms are those for my new residue. For next step I get more constraint deviation. Now, is it possible that this is because of wrong parameters? Or maybe I should minimize my system further? Here are all the files: http://www.speedyshare.com/jjvgd/md-simul.tar.bz2 When sharing files, please only post what is actually necessary to reproduce the problem - a self-contained force field directory, coordinates, topology, .mdp, and index file if needed. A dump of dozens of files with no context gets burdensome to go through. Your minimized geometry is clearly junk. Just visualize the structure and you will see that your mCherry residue is completely distorted. The very large (10^4) force after EM should have been the first clue that something is very wrong. The problems almost certainly stem from the manipulations you've made to the angles and dihedrals. I don't understand why you've commented some of them out. For instance, the first angle that you've removed is atoms 977-978-992, which clearly should have an angle interaction because 977-978 and 978-992 are bonded. Simply removing inconvenient interactions (i.e. lacking parameters or whatever) leads to a total meltdown of the model. -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
Re: [gmx-users] grompp erros
On 7/2/14, 5:39 AM, Linlin Sun wrote: Hello everyone, In order to build a virtual site which is independent from other structure, I have created a new atom type and set the mass of this new atom type to zero. However, when I use* grompp*, it failed with fatal errors, which complain about the zero mass of the new atom type. Anyone could possibly know how to get around this problem? Any suggestions would be helpful. Thanks very much! If you've declared it as an atom (particle type A), then that's probably why you're getting this error. Virtual site types are particle type V in ffnonbonded.itp. I guess the larger point is - why have a virtual site that is not dependent upon any other elements of the structure? -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] Use trjconv in parallel
Thanks for your quick and also fast (;)) reply, Carsten. Stéphane -- Message: 4 Date: Wed, 2 Jul 2014 10:55:45 + From: ABEL Stephane 175950 stephane.a...@cea.fr To: gromacs.org_gmx-users@maillist.sys.kth.se gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Use trjconv in parallel, Message-ID: 3e39b768bb199548ab18f7289e7534af1b24f...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=iso-8859-1 Hello, in short : it is possible ? I use the gromacs v4.6.5. Thanks St?phane -- Message: 5 Date: Wed, 2 Jul 2014 13:44:08 +0200 From: Carsten Kutzner ckut...@gwdg.de To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Use trjconv in parallel, Message-ID: 39b862ce-6e52-4590-9c57-ba34864b2...@gwdg.de Content-Type: text/plain; charset=iso-8859-1 On 02 Jul 2014, at 12:55, ABEL Stephane 175950 stephane.a...@cea.fr wrote: Hello, in short : it is possible ? I use the gromacs v4.6.5. No. Carsten Thanks St?phane -- 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. -- Message: 6 Date: Wed, 02 Jul 2014 07:50:34 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] grompp does not find atomtype Message-ID: 53b3f20a.7060...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 7/2/14, 4:40 AM, Dawid das wrote: I have managed to deal with this problem in following way: In topology file some bonding parameters were actually missing but some bonding parameters were not needed, e.g. U-B or dihedral parameters for atoms which are not connected, that is they belong to different parts of my new residue. I found parameters for the missing ones and hashed (;) them out. Is it what I can do? Like I say, theses bonding parameters that I hashed out were for atom types which are not connected directly. Then I performed minimization with steepest descent and in output file I got: 4655e+05 Fmax= 6.53501e+03, atom= 1003^MStep= 426, Dmax= 2.5e-06 nm, Epot= -4.54655e+05 Fmax= 9.45125e+03, atom= 1003^MStep= 427, Dmax= 1.2e-06 nm, Epot= -4.54655e+05 Fmax= 1.25724e+04, atom= 1003^M Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 428 steps, but did not reach the requested Fmax 1000. Potential Energy = -4.5465475e+05 Maximum force = 1.7057922e+04 on atom 1003 Norm of force = 1.1677969e+02 But I continued with NVT MD simulation. This is my nvt-md.mdp file: title = NVT MD integrator = md constraints = all-bonds dt = 0.001 nsteps = 2 nstenergy = 100 nstlist = 10 nstxout = 1000 nstvout = 1000 nstfout = 0 nstlog = 100 nstxtcout = 1000 xtcprecision= 500 ns_type = grid coulombtype = PME rlist = 1.0 rcoulomb= 1.0 rvdw= 1.0 These cutoffs are incorrect for using CHARMM force fields. See previous posts on proper settings. tcoupl = nose-hoover tc-grps = Protein SOL NA tau_t = 0.1 0.1 0.1 ;(3 numbers - because 3 tc-grps) ref_t = 100 100 100 ;(3 numbers - because 3 tc-grps) Coupling water and ions separately is not sensible. http://www.gromacs.org/Documentation/Terminology/Thermostats#What_Not_To_Do Pcoupl = No gen_vel = yes gen_temp= 100 gen_seed= 173529 energygrps = Protein SOL NA constraint_algorithm = LINCS pbc = xyz And in my NVT output I got error for LINCS: relative constraint deviation after LINCS: rms 0.036755, max 1.509884 (between atoms 998 and 1000) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 1001 1003 62.10.1410 0.2032 0.1410 1001 1002 68.10.1240 0.1962 0.1240 1000 1001 88.10.1460 0.3276 0.1460 998 1000 90.00.1390 0.3489 0.1390 986 1000 90.70.1400 0.2237 0.1400 985986 30.70.1300 0.1499 0.1300 Wrote pdb files with previous and current coordinates These atoms are those for my new residue. For next step
[gmx-users] Problem with g_chi options
Hi, I want do an analysis of my simulation with the tool g_chi. The problem is, that the optional output options don't work. I use the following command: g_chi -s config.gro -f traj.xtc -oh -all and all I get are the standard output files chi.log and order.xvg. I am not sure if it has something to do with the following warning I get: WARNING: not all dihedrals found in topology (only 1056 out of 1746)! Honestly, I don't understand why I get this warning, because all the input files are fine. Thanks for your help! Best regards, Anna -- 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] grompp does not find atomtype
On 7/2/14, 9:22 AM, Dawid das wrote: 2014-07-02 13:50 GMT+02:00 Justin Lemkul jalem...@vt.edu: The problems almost certainly stem from the manipulations you've made to the angles and dihedrals. I don't understand why you've commented some of them out. For instance, the first angle that you've removed is atoms 977-978-992, which clearly should have an angle interaction because 977-978 and 978-992 are bonded. Simply removing inconvenient interactions (i.e. lacking parameters or whatever) leads to a total meltdown of the model. Okey, but what should I do if there are missing parameters for combination of atoms which are not bonded? For instance: 973-977-978-992 atoms are not bonded but still in *top there is an torsion interaction for these atoms? What does it mean? It seems like some of the atom types are confused? Is it possible that I defined them in ambigous way? Introduction of custom atom types requires introduction of associated bonded parameters. You can't introduce atoms without defining all the ways that they interact. The proper approach is to add suitable parameters in ffbonded.itp or in the .top itself. If you don't have those parameters, you need to derive them or obtain them from some reliable source. -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] grompp does not find atomtype
Beside that, why do you say that 978-992 are bonded? According to visual inspection of mCherry7-solv-ion.gro there is no connection between them (as it should be) and also in mCherry7.top there is no bonding parameter for them. 2014-07-02 15:22 GMT+02:00 Dawid das add...@googlemail.com: 2014-07-02 13:50 GMT+02:00 Justin Lemkul jalem...@vt.edu: The problems almost certainly stem from the manipulations you've made to the angles and dihedrals. I don't understand why you've commented some of them out. For instance, the first angle that you've removed is atoms 977-978-992, which clearly should have an angle interaction because 977-978 and 978-992 are bonded. Simply removing inconvenient interactions (i.e. lacking parameters or whatever) leads to a total meltdown of the model. Okey, but what should I do if there are missing parameters for combination of atoms which are not bonded? For instance: 973-977-978-992 atoms are not bonded but still in *top there is an torsion interaction for these atoms? What does it mean? It seems like some of the atom types are confused? Is it possible that I defined them in ambigous way? -- 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] grompp does not find atomtype
Excuse me but I don't think we understand each other. If there are three atoms for instance and two of them are bonded and the third is not then how can I obtain or derive parameters for them? That is what I do not understand. 2014-07-02 15:29 GMT+02:00 Dawid das add...@googlemail.com: Beside that, why do you say that 978-992 are bonded? According to visual inspection of mCherry7-solv-ion.gro there is no connection between them (as it should be) and also in mCherry7.top there is no bonding parameter for them. 2014-07-02 15:22 GMT+02:00 Dawid das add...@googlemail.com: 2014-07-02 13:50 GMT+02:00 Justin Lemkul jalem...@vt.edu: The problems almost certainly stem from the manipulations you've made to the angles and dihedrals. I don't understand why you've commented some of them out. For instance, the first angle that you've removed is atoms 977-978-992, which clearly should have an angle interaction because 977-978 and 978-992 are bonded. Simply removing inconvenient interactions (i.e. lacking parameters or whatever) leads to a total meltdown of the model. Okey, but what should I do if there are missing parameters for combination of atoms which are not bonded? For instance: 973-977-978-992 atoms are not bonded but still in *top there is an torsion interaction for these atoms? What does it mean? It seems like some of the atom types are confused? Is it possible that I defined them in ambigous way? -- 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] grompp does not find atomtype
On 7/2/14, 9:29 AM, Dawid das wrote: Beside that, why do you say that 978-992 are bonded? According to visual inspection of mCherry7-solv-ion.gro there is no connection between them (as it should be) and also in mCherry7.top there is no bonding parameter for them. Inspection of a coordinate file tells you nothing about the bonded structure. Look at the topology, line 4712: 978 992 10.1350 127612.0 That says atoms 978 and 992 are bonded, and you have defined the parameters for that bond manually. -Justin 2014-07-02 15:22 GMT+02:00 Dawid das add...@googlemail.com: 2014-07-02 13:50 GMT+02:00 Justin Lemkul jalem...@vt.edu: The problems almost certainly stem from the manipulations you've made to the angles and dihedrals. I don't understand why you've commented some of them out. For instance, the first angle that you've removed is atoms 977-978-992, which clearly should have an angle interaction because 977-978 and 978-992 are bonded. Simply removing inconvenient interactions (i.e. lacking parameters or whatever) leads to a total meltdown of the model. Okey, but what should I do if there are missing parameters for combination of atoms which are not bonded? For instance: 973-977-978-992 atoms are not bonded but still in *top there is an torsion interaction for these atoms? What does it mean? It seems like some of the atom types are confused? Is it possible that I defined them in ambigous way? -- == 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] Changed order of molecules in top
Justin Lemkul jalemkul@... writes: On 7/2/14, 3:31 AM, Emma Ahlstrand wrote: Hi, I have a problem with that the order of atoms in my topology does not match the order of atoms in the gro-file. I use amber99sb and I have built itp-files on my own for the molecules that are not present in the library. Each IMI contains 9 atoms and each SOL 3 atoms and the ZN is one atom so in total it should be 9*2+3*2+1=25 atoms in total, which is present in the .gro file, but when I run with the topology-file pasted below I get a error the this file contains 34 atoms. This is my topologyfile: ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Additional atom types [ atomtypes ] ; name at_name at_num mass charge ptype sigmaepsilon ; sw ref Zn++ Zn++30 65.37000 2.000A1.94216e-01 1.046 ; 1Stote Proteins 23:12 1995 ; Include topology for ions #include zn.itp ; Include water topology #include spcetestamber.itp ; Include topology for imidazole #include imiamberrtp.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [system ] ; Name ZnHis2Wa2 [ molecules ] ; Compound#mols ZN2+ 1 IMI 2 SOL 2 - Fatal error: number of coordinates in coordinate file (ZnHis2Wa2optM06.gro, 25) does not match topology (ZnHis2Wa2optM06amber.top, 34) Since the difference is 9 atoms, I thought that the difference is one IMI, so I tried with one less IMI in the topology, printed below. ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Additional atom types [ atomtypes ] ; name at_name at_num mass charge ptype sigmaepsilon ; sw ref Zn++ Zn++30 65.37000 2.000A1.94216e-01 1.046 ; 1Stote Proteins 23:12 1995 ; Include topology for ions #include zn.itp ; Include water topology #include spcetestamber.itp ; Include topology for imidazole #include imiamberrtp.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [system ] ; Name ZnHis2Wa2 [ molecules ] ; Compound#mols ZN2+ 1 IMI 1 SOL 2 Then the number of atoms matches, but I get the information that the atom names does not match. Warning: atom name 1 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro does not match (C1 - ZN) Warning: atom name 2 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro does not match (N1 - C1) By this message it gets clear to me that the topology makes an IMI first and then go on to the ZN and then probably the IMI and the two waters specified in the top-file. Why does it do that? And how do I correct it? No, your coordinate file has IMI first. grompp expects the input coordinates and topology to be in the same order. You list Zn, IMI, and SOL in the .top - that is the expected order in the coordinates. As reported by grompp, that is not the case. There should be no probably here; with such a small system it should be very easy to inspect the .gro file in a text editor and see precisely what is going on. -Justin Hi Justin, the problem is that my coordinate file (ZnHis2Wa2optM06.gro) has Zn first and then two IMI and then two water and this is what I think I make with my topology file as well, but the topology seems to produce an IMI first? ZnHis2Wa2 25 1Zn++ZN1 1.495 1.497 1.361 2MOL C12 1.293 1.499 1.588 2MOL N13 1.324 1.561 1.451 2MOL C24 1.166 1.556 1.632 ... Regards, Emma -- 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] Changed order of molecules in top
On 7/2/14, 9:48 AM, Emma A wrote: Justin Lemkul jalemkul@... writes: On 7/2/14, 3:31 AM, Emma Ahlstrand wrote: Hi, I have a problem with that the order of atoms in my topology does not match the order of atoms in the gro-file. I use amber99sb and I have built itp-files on my own for the molecules that are not present in the library. Each IMI contains 9 atoms and each SOL 3 atoms and the ZN is one atom so in total it should be 9*2+3*2+1=25 atoms in total, which is present in the .gro file, but when I run with the topology-file pasted below I get a error the this file contains 34 atoms. This is my topologyfile: ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Additional atom types [ atomtypes ] ; name at_name at_num mass charge ptype sigmaepsilon ; sw ref Zn++ Zn++30 65.37000 2.000A1.94216e-01 1.046 ; 1Stote Proteins 23:12 1995 ; Include topology for ions #include zn.itp ; Include water topology #include spcetestamber.itp ; Include topology for imidazole #include imiamberrtp.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [system ] ; Name ZnHis2Wa2 [ molecules ] ; Compound#mols ZN2+ 1 IMI 2 SOL 2 - Fatal error: number of coordinates in coordinate file (ZnHis2Wa2optM06.gro, 25) does not match topology (ZnHis2Wa2optM06amber.top, 34) Since the difference is 9 atoms, I thought that the difference is one IMI, so I tried with one less IMI in the topology, printed below. ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Additional atom types [ atomtypes ] ; name at_name at_num mass charge ptype sigmaepsilon ; sw ref Zn++ Zn++30 65.37000 2.000A1.94216e-01 1.046 ; 1Stote Proteins 23:12 1995 ; Include topology for ions #include zn.itp ; Include water topology #include spcetestamber.itp ; Include topology for imidazole #include imiamberrtp.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [system ] ; Name ZnHis2Wa2 [ molecules ] ; Compound#mols ZN2+ 1 IMI 1 SOL 2 Then the number of atoms matches, but I get the information that the atom names does not match. Warning: atom name 1 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro does not match (C1 - ZN) Warning: atom name 2 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro does not match (N1 - C1) By this message it gets clear to me that the topology makes an IMI first and then go on to the ZN and then probably the IMI and the two waters specified in the top-file. Why does it do that? And how do I correct it? No, your coordinate file has IMI first. grompp expects the input coordinates and topology to be in the same order. You list Zn, IMI, and SOL in the .top - that is the expected order in the coordinates. As reported by grompp, that is not the case. There should be no probably here; with such a small system it should be very easy to inspect the .gro file in a text editor and see precisely what is going on. -Justin Hi Justin, the problem is that my coordinate file (ZnHis2Wa2optM06.gro) has Zn first and then two IMI and then two water and this is what I think I make with my topology file as well, but the topology seems to produce an IMI first? ZnHis2Wa2 25 1Zn++ZN1 1.495 1.497 1.361 2MOL C12 1.293 1.499 1.588 2MOL N13 1.324 1.561 1.451 2MOL C24 1.166 1.556 1.632 ... Without seeing the full contents of all the files, none of this really makes sense. If you can provide a link to download the full (1) topology and all related .itp files, (2) coordinates, and (3) .mdp files, I will take a look. -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.
[gmx-users] Graphene topology file
Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial. http://chembytes.wikidot.com/grocnt But I think this tutorial is quite old and hence suitable for older version of gromacs as it still uses FF.dat file. Moreover if i am trying to make a new forcefield directory with name graphite_oplsaa containing the modified files like .n2t,.rtp and .itp, its giving me an error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. When I try to add this forcefield in original path ie. user/share/gromacs/top, it does not allow me to do that as i am not the administrator. Can anyone please let me know how to create the topology file. I require 3 graphene sheets with pbc. I have created the .pdb file using nanobuilder in vmd. Thanks and Regards Sukriti [https://encrypted-tbn2.gstatic.com/images?q=tbn:ANd9GcQuwIkOr74lrv1_LpOuPBiUQ7Ai2kV8dmaAKtXKB0KYMUKxiIHSJg] http://www.google.com/imgres?imgurl=http%3A%2F%2Fwww.spms.ntu.edu.sg%2Fmas%2Fconference%2Ficits2013%2FICITS-2013-files%2Fntu-logo.jpgimgrefurl=http%3A%2F%2Fwww.spms.ntu.edu.sg%2Fmas%2Fconference%2Ficits2013%2Fh=59w=150tbnid=dMsKki52xFWVeM%3Azoom=1docid=XqAK8OLvcu_FUMei=xVyyU5q9A87j8AWMzYG4Cwtbm=ischved=0CFgQMygxMDEiact=rcuact=3dur=1673page=3start=41ndsp=27 Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University http://maps.ntu.edu.sg/maps#q:research%20techno%20plaza%20%28rtp%29 Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sgmailto:xx...@e.ntu.edu.sg | Web:erian.ntu.edu.sg http://www.ntu.edu.sg/home/xuzc/People.html -- 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] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters
Dear Justin, Thank you very much for your reply. I have tried the converter but I think I don't have enough experience to get the CHARMM files working properly with the converter. If I sent you the files, would it be possible to do it for me or guide me through it? Thanks again, Nicholas On 23 June 2014 17:42, Justin Lemkul jalem...@vt.edu wrote: On 6/23/14, 9:48 AM, Nikolaos Michelarakis wrote: Dear All, First, I would like to say that I have started using GROMACS during this last month so please take that in mind when answering. I am trying to run an MD simulation of an enzyme which contains some non standard residues such as a tungsten metal ion and some other cofactors. I understand that I need to create the topology and find the parameters for these non-standard residues. Reading the manual I saw about .itp files and, correct me if I'm wrong, but it's my understanding that these are used for parts of the topology which are not bonded or intergrated in the structure that is being simulated. My question is how do I include these bonded parts in the simulation? An .itp file specifies a distinct [moleculetype] that shares no bonded interactions with any other species in the system. The development version of the code has the capability to do intermolecular bondeds, but at present the distinction is true enough. Are you asking how to include actual bonds between your non-standard residues and other parts of the system? If so, then the only options are: 1. Create an .rtp entry for your non-standard residue(s) and modify specbond.dat accordingly, as these will likely be non-linear bonds. That way, you'll have a single [moleculetype] in which you will have bonds between the different residues. 2. Use git to obtain the developmental version of the code that has intermolecular bond capabilities. I don't recall offhand which patch has it or if it's even been merged, but it's in the Gerrit repo, at least. My second question, someone has already developed a topology and some parameters for this structure but in CHARM. I tried using one of the two scripts available online to convert them to GROMACS but to no avail. Is there a way to automatically do this or will I have to go all over it by hand? If you have a stream file, we have a converter: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs It was designed to interface with CGenFF .str files from ParamChem, but it should do the job. -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. -- 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] Changed order of molecules in top
Without seeing the full contents of all the files, none of this really makes sense. If you can provide a link to download the full (1) topology and all related .itp files, (2) coordinates, and (3) .mdp files, I will take a look. -Justin Hi again, thanks a lot for taking your time. Here is a link to the top (and test.top with just one IMI), the gro, the itp´s, and the mdp files. https://www.dropbox.com/s/dmz41drsjr0bqkn/ZnHis2Wa2.tar.gz I hope this kind of link works. Best regards, Emma -- 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] Changed order of molecules in top
On 7/2/14, 11:17 AM, Emma A wrote: Without seeing the full contents of all the files, none of this really makes sense. If you can provide a link to download the full (1) topology and all related .itp files, (2) coordinates, and (3) .mdp files, I will take a look. -Justin Hi again, thanks a lot for taking your time. Here is a link to the top (and test.top with just one IMI), the gro, the itp´s, and the mdp files. https://www.dropbox.com/s/dmz41drsjr0bqkn/ZnHis2Wa2.tar.gz I hope this kind of link works. Best regards, Emma Here's your problem: [ molecules ] ; Compound#mols IMI 1 is in imiamberrtp.itp and it should not be. An .itp file specifies a [moleculetype] and associated parameters. The [system] and [molecules] directives are system-level instructions. So what's happening is you're telling grompp that there is an IMI molecule as soon as you #include the .itp file. A bit surprising that there aren't any other fatal errors, because technically this breaks the topology order. Remove [system] and [molecules] from this .itp file, correct the [molecules] directive to specify 2 IMI in the .top, and you should be fine. -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] Graphene topology file
On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote: Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial. http://chembytes.wikidot.com/grocnt But I think this tutorial is quite old and hence suitable for older version of gromacs as it still uses FF.dat file. Moreover if i am trying to make a new forcefield directory with name graphite_oplsaa containing the modified files like .n2t,.rtp and .itp, its giving me an error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. When I try to add this forcefield in original path ie. user/share/gromacs/top, it does not allow me to do that as i am not the administrator. Can anyone please let me know how to create the topology file. I require 3 graphene sheets with pbc. I have created the .pdb file using nanobuilder in vmd. The tutorial is indeed outdated but the logic is fairly sound. You don't have to modify anything in $GMXLIB (system-wide); you can just create an .n2t file in the working directory and it will override the one at the force field level. -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] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters
On 7/2/14, 10:55 AM, Nikolaos Michelarakis wrote: Dear Justin, Thank you very much for your reply. I have tried the converter but I think I don't have enough experience to get the CHARMM files working properly with the converter. If I sent you the files, would it be possible to do it for me or guide me through it? If you post exactly what you're doing and exactly what the output/error is, I might be able to spot the problem. -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.
[gmx-users] Requesting help on converting a CG (coarse grained) trajectory to a FG (fine grained) trajectory
Hi all, I have just ran a CG MD with the Martini force field, and I was wondering if it’s possible to transform this CG trajectory back to a FG trajectory? If it’s possible, are there any available tutorials I can follow? If not, please guide me on the commands and modules required to execute this action. Thanks, any help is greatly appreciated. =) Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry Biological Chemistry School of Physical Mathematical Sciences | Nanyang Technological University | Singapore 639798 Tel: (+65) 97967803 | Email: yipy0...@e.ntu.edu.sg | GMT+8h -- 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] Requesting help on converting a CG (coarse grained) trajectory to a FG (fine grained) trajectory
On 7/2/14, 11:48 AM, Yip Yew Mun wrote: Hi all, I have just ran a CG MD with the Martini force field, and I was wondering if it’s possible to transform this CG trajectory back to a FG trajectory? If it’s possible, are there any available tutorials I can follow? If not, please guide me on the commands and modules required to execute this action. http://md.chem.rug.nl/cgmartini/index.php/others#Reverse-transformation -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 5.0 official release
Hey Mark, This might be a a dumb question, but over the official release download links on the gromacs website, it still says: Please note that these are not yet regarded as production quality, pending further testing, but the code is now feature-stable. Is this a typo because I thought the official release is production quality. Best Wishes, Ali Khan On Sun, Jun 29, 2014 at 4:53 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi GROMACS users, The official release of GROMACS 5.0 is available! What new things can you expect? * GROMACS now uses a combination of *C++98* and C99, so you will need a working C++ compiler that is intended to work with your C compiler * Building GROMACS now requires *CMake version 2.8.8*, which will mean some of you will need to update your version in order to build GROMACS. * The native GPU port available in GROMACS 4.6 supports a wider range of simulation types, and now requires CUDA 4.0 * The *Verlet cut-off scheme is now the default* in GROMACS. One of our design principles is that GROMACS will do correct simulations by default, and the use of this scheme makes that easy and fast. The group cut-off scheme will be removed in a future version, so start planning for that! * You can now treat *Lennard-Jones interactions with PME*, which is expected to provide a much better treatment of spatially heterogeneous long-ranged dispersion interactions at cost comparable to that of a cutoff. LJPME is supported for both cut-off schemes, and almost all kinds of simullations * GROMACS deploys the Random123 stateless random-number generator * GROMACS now uses the stochastic dynamics (sd1) integrator of Goga Berendsen * GROMACS tools are now bundled together into *just two binaries* - mdrun and gmx. The latter contains most of the tools familiar to you, perhaps with new names, and a couple of new ones. For the time being, the install procedure will also create symbolic links so that your old scripts will keep working for a time, but these will go away at some future point! * There is support for the new TNG compressed trajectory format * GROMACS contains a feature for computational electrophysiology simulations, to simulate a steady-state ion concentration difference between compartments of a double membrane * GROMACS supports some special interactions for coarse-grained interactions with Martini force fields * GROMACS support for Interactive Molecular Dynamics (IMD) * A handful of the tools have been re-implemented using a *new C++ analysis framework*, which we hope will provide a better platform for maintaining and adding to their functionality in the future. * There is an enhanced testing suite, with *unit tests* for most new C++ code. * There is preliminary support for Intel Xeon Phi (only in native mode, and performance will only be slightly improved) * GROMACS has removed support for particle decomposition - the simulation types that required it are now limited to a single MPI rank (but perhaps multiple OpenMP threads) Please see the link to the release notes below for more details. All the content of GROMACS 4.6.6 (whose release is imminent) is present, apart from features that have been removed. You can find the code, manual, release notes, installation instructions and test suite at the links below. ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-5.0.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0 http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0 http://gerrit.gromacs.org/download/regressiontests-5.0.tar.gz Happy simulating! Mark Abraham GROMACS development manager -- 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 5.0 official release
On Jul 2, 2014 6:44 PM, Ali Khan ak...@virginia.edu wrote: Hey Mark, This might be a a dumb question, but over the official release download links on the gromacs website, it still says: Please note that these are not yet regarded as production quality, pending further testing, but the code is now feature-stable. Is this a typo because I thought the official release is production quality. Indeed, they are. I have fixed my copy-paste error, now. Sorry about that! Mark Best Wishes, Ali Khan On Sun, Jun 29, 2014 at 4:53 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi GROMACS users, The official release of GROMACS 5.0 is available! What new things can you expect? * GROMACS now uses a combination of *C++98* and C99, so you will need a working C++ compiler that is intended to work with your C compiler * Building GROMACS now requires *CMake version 2.8.8*, which will mean some of you will need to update your version in order to build GROMACS. * The native GPU port available in GROMACS 4.6 supports a wider range of simulation types, and now requires CUDA 4.0 * The *Verlet cut-off scheme is now the default* in GROMACS. One of our design principles is that GROMACS will do correct simulations by default, and the use of this scheme makes that easy and fast. The group cut-off scheme will be removed in a future version, so start planning for that! * You can now treat *Lennard-Jones interactions with PME*, which is expected to provide a much better treatment of spatially heterogeneous long-ranged dispersion interactions at cost comparable to that of a cutoff. LJPME is supported for both cut-off schemes, and almost all kinds of simullations * GROMACS deploys the Random123 stateless random-number generator * GROMACS now uses the stochastic dynamics (sd1) integrator of Goga Berendsen * GROMACS tools are now bundled together into *just two binaries* - mdrun and gmx. The latter contains most of the tools familiar to you, perhaps with new names, and a couple of new ones. For the time being, the install procedure will also create symbolic links so that your old scripts will keep working for a time, but these will go away at some future point! * There is support for the new TNG compressed trajectory format * GROMACS contains a feature for computational electrophysiology simulations, to simulate a steady-state ion concentration difference between compartments of a double membrane * GROMACS supports some special interactions for coarse-grained interactions with Martini force fields * GROMACS support for Interactive Molecular Dynamics (IMD) * A handful of the tools have been re-implemented using a *new C++ analysis framework*, which we hope will provide a better platform for maintaining and adding to their functionality in the future. * There is an enhanced testing suite, with *unit tests* for most new C++ code. * There is preliminary support for Intel Xeon Phi (only in native mode, and performance will only be slightly improved) * GROMACS has removed support for particle decomposition - the simulation types that required it are now limited to a single MPI rank (but perhaps multiple OpenMP threads) Please see the link to the release notes below for more details. All the content of GROMACS 4.6.6 (whose release is imminent) is present, apart from features that have been removed. You can find the code, manual, release notes, installation instructions and test suite at the links below. ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-5.0.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_5.0.x#Release_notes_for_5.0 http://www.gromacs.org/Documentation/Installation_Instructions_for_5.0 http://gerrit.gromacs.org/download/regressiontests-5.0.tar.gz Happy simulating! Mark Abraham GROMACS development manager -- 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
Re: [gmx-users] [gmx-announce] GROMACS 5.0 official release
Hi, The warnings are not a problem - gmx view does not get as much love as the rest of the project! Mark On Jul 2, 2014 11:23 AM, Luís Pereira luisp2...@gmail.com wrote: Hi, Thank you for this new version! When compiling we've got these warnings: attribute warn_unused_result [-Wunused-result] fscanf(in, %6s, buf); ^ /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:391:28: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(in, %15s, buf); ^ /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:412:36: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(in, %15s, buf); ^ /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:416:40: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(in, %15s, buf); ^ /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:435:36: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(in, %15s, buf); ^ /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:439:32: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(in, %15s, buf); ^ /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp: In function ‘void ReadAccOpen(const char*, FILE*)’: /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:106:27: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(in, %4s, buf); ^ /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp: In function ‘void ReadAccClose(const char*, FILE*)’: /home/arh/Downloads/gromacs-5.0/src/programs/view/fgrid.cpp:117:27: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(in, %4s, buf); ^ OS is ubuntu 14.04 64 bit, virtualbox machine: GROMACS: gmx, VERSION 5.0 Executable: /usr/local/gromacs/bin/gmx Library dir: /usr/local/gromacs/share/gromacs/top Command line: gmx -version Gromacs version:VERSION 5.0 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) SIMD instructions: SSE2 FFT library:fftw-3.3.3-sse2-avx RDTSCP usage: enabled C++11 compilation: enabled TNG support:enabled Tracing support:disabled Built on: Qua Jul 2 09:54:48 WEST 2014 Built by: arh@arh-VirtualBox [CMAKE] Build OS/arch: Linux 3.13.0-24-generic x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU E5530 @ 2.40GHz Build CPU family: 6 Model: 26 Stepping: 5 Build CPU features: apic clfsh cmov cx8 lahf_lm mmx msr pse rdtscp sse2 sse3 ssse3 C compiler: /usr/bin/cc GNU 4.8.2 C compiler flags:-msse2 -Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG C++ compiler: /usr/bin/c++ GNU 4.8.2 C++ compiler flags: -msse2 -std=c++0x -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast -Wno-array-bounds -O3 -DNDEBUG Boost version: 1.55.0 (internal) On 29 June 2014 21:53, Mark Abraham mark.j.abra...@gmail.com wrote: Hi GROMACS users, The official release of GROMACS 5.0 is available! What new things can you expect? * GROMACS now uses a combination of *C++98* and C99, so you will need a working C++ compiler that is intended to work with your C compiler * Building GROMACS now requires *CMake version 2.8.8*, which will mean some of you will need to update your version in order to build GROMACS. * The native GPU port available in GROMACS 4.6 supports a wider range of simulation types, and now requires CUDA 4.0 * The *Verlet cut-off scheme is now the default* in GROMACS. One of our design principles is that GROMACS will do correct simulations by default, and the
Re: [gmx-users] Regarding lipid topology
Thank you Sir. Sorry for the late reply. So, the changes like dihedral angle for C8-C9=C10-C11 should be 180 instead of 0 in trans state. Are there any other adjustments I should make to build the trans lipid isomer topology from cis? Thank you for your valuable time and concern. On Mon, Jun 16, 2014 at 4:44 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: Of course, no. You need to adjust your topology (force field?) to distinguish between cis- and trans- states. Dr. Vitaly V. Chaban On Mon, Jun 16, 2014 at 11:03 AM, Venkat Reddy venkat...@gmail.com wrote: Dear all, I want to simulate a membrane protein system. My membrane is composed of DOPC (cis isomer) and DEPC (trans isomer). I have downloaded DOPC topology from lipidbook website. Since DOPC and DEPC are isomers, can I use the topology of DOPC for DEPC also? Thank and regards 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. -- 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.
[gmx-users] Gromacs 5.0 download
I know this is a silly question but in the downloads section when I click to download it the new window opens and 0bit tar file is downloaded.I switched to windows but even then the new tab doesn't show anything.I don't understand why is this happening. -- 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 5.0 download
The link is correct, something must be broken on your side. Try using e.g. wget: $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l gromacs*.gz --2014-07-02 22:34:44-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz = `gromacs-5.0.tar.gz' Resolving ftp.gromacs.org... 130.238.41.205 Connecting to ftp.gromacs.org|130.238.41.205|:21... connected. Logging in as anonymous ... Logged in! == SYST ... done.== PWD ... done. == TYPE I ... done. == CWD (1) /pub/gromacs ... done. == SIZE gromacs-5.0.tar.gz ... 26862408 == PASV ... done.== RETR gromacs-5.0.tar.gz ... done. Length: 26862408 (26M) (unauthoritative) 100%[] 26,862,408 28.6M/s in 0.9s 2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408] Cheers, -- Szilárd On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh harshsingh2...@gmail.com wrote: I know this is a silly question but in the downloads section when I click to download it the new window opens and 0bit tar file is downloaded.I switched to windows but even then the new tab doesn't show anything.I don't understand why is this happening. -- 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 5.0 download
Maybe something on your end is blocking ftp connections. You can download from a mirror such as: http://fossies.org/linux/privat/gromacs-5.0.tar.gz If you download from a mirror make sure to check the md5sum. On Wed, Jul 2, 2014 at 4:36 PM, Szilárd Páll pall.szil...@gmail.com wrote: The link is correct, something must be broken on your side. Try using e.g. wget: $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l gromacs*.gz --2014-07-02 22:34:44-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz = `gromacs-5.0.tar.gz' Resolving ftp.gromacs.org... 130.238.41.205 Connecting to ftp.gromacs.org|130.238.41.205|:21... connected. Logging in as anonymous ... Logged in! == SYST ... done.== PWD ... done. == TYPE I ... done. == CWD (1) /pub/gromacs ... done. == SIZE gromacs-5.0.tar.gz ... 26862408 == PASV ... done.== RETR gromacs-5.0.tar.gz ... done. Length: 26862408 (26M) (unauthoritative) 100%[] 26,862,408 28.6M/s in 0.9s 2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408] Cheers, -- Szilárd On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh harshsingh2...@gmail.com wrote: I know this is a silly question but in the downloads section when I click to download it the new window opens and 0bit tar file is downloaded.I switched to windows but even then the new tab doesn't show anything.I don't understand why is this happening. -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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 5.0 download
Yeah apparently the ftp connection is blocked.I actually forgot that.Thanks for the help. On Thu, Jul 3, 2014 at 2:16 AM, Roland Schulz rol...@utk.edu wrote: Maybe something on your end is blocking ftp connections. You can download from a mirror such as: http://fossies.org/linux/privat/gromacs-5.0.tar.gz If you download from a mirror make sure to check the md5sum. On Wed, Jul 2, 2014 at 4:36 PM, Szilárd Páll pall.szil...@gmail.com wrote: The link is correct, something must be broken on your side. Try using e.g. wget: $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l gromacs*.gz --2014-07-02 22:34:44-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz = `gromacs-5.0.tar.gz' Resolving ftp.gromacs.org... 130.238.41.205 Connecting to ftp.gromacs.org|130.238.41.205|:21... connected. Logging in as anonymous ... Logged in! == SYST ... done.== PWD ... done. == TYPE I ... done. == CWD (1) /pub/gromacs ... done. == SIZE gromacs-5.0.tar.gz ... 26862408 == PASV ... done.== RETR gromacs-5.0.tar.gz ... done. Length: 26862408 (26M) (unauthoritative) 100%[] 26,862,408 28.6M/s in 0.9s 2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408] Cheers, -- Szilárd On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh harshsingh2...@gmail.com wrote: I know this is a silly question but in the downloads section when I click to download it the new window opens and 0bit tar file is downloaded.I switched to windows but even then the new tab doesn't show anything.I don't understand why is this happening. -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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. -- Harshkumar Singh 2nd Year Integrated MSc Chemistry IIT Bombay. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] g_polystat sorts the eigen vector
Dear gmx users, The g_polystat tool arranges the Rg eigen vectors in the descending order. We cannot see how a particular eigen vector (one along the X-axis) varies with time. We can obviously comment the section of the g_polystat code to avoid the sorting. Is there a reason, why do we sort the eigen vectors? It would be helpful if someone help me to understand this. Thanks Chandan -- 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] Gromacs 5.0 download
On 7/2/14, 4:36 PM, Szilárd Páll wrote: The link is correct, something must be broken on your side. Try using e.g. wget: $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l gromacs*.gz --2014-07-02 22:34:44-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz = `gromacs-5.0.tar.gz' Resolving ftp.gromacs.org... 130.238.41.205 Connecting to ftp.gromacs.org|130.238.41.205|:21... connected. Logging in as anonymous ... Logged in! == SYST ... done.== PWD ... done. == TYPE I ... done. == CWD (1) /pub/gromacs ... done. == SIZE gromacs-5.0.tar.gz ... 26862408 == PASV ... done.== RETR gromacs-5.0.tar.gz ... done. Length: 26862408 (26M) (unauthoritative) 100%[] 26,862,408 28.6M/s in 0.9s I'm having a similar problem as the OP. The web interface just seems to hang and using wget takes over an hour with a download rate of 4 KB/sec. This is true at work (hardwired workstation) and at home (laptop on wifi) -Justin 2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408] Cheers, -- Szilárd On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh harshsingh2...@gmail.com wrote: I know this is a silly question but in the downloads section when I click to download it the new window opens and 0bit tar file is downloaded.I switched to windows but even then the new tab doesn't show anything.I don't understand why is this happening. -- 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] Gromacs 5.0 download
On Wed, Jul 2, 2014 at 11:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/2/14, 4:36 PM, Szilárd Páll wrote: The link is correct, something must be broken on your side. Try using e.g. wget: $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l gromacs*.gz --2014-07-02 22:34:44-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz = `gromacs-5.0.tar.gz' Resolving ftp.gromacs.org... 130.238.41.205 Connecting to ftp.gromacs.org|130.238.41.205|:21... connected. Logging in as anonymous ... Logged in! == SYST ... done.== PWD ... done. == TYPE I ... done. == CWD (1) /pub/gromacs ... done. == SIZE gromacs-5.0.tar.gz ... 26862408 == PASV ... done.== RETR gromacs-5.0.tar.gz ... done. Length: 26862408 (26M) (unauthoritative) 100%[] 26,862,408 28.6M/s in 0.9s I'm having a similar problem as the OP. The web interface just seems to hang and using wget takes over an hour with a download rate of 4 KB/sec. This is true at work (hardwired workstation) and at home (laptop on wifi) OK, that's alarming. Perhaps uu.se (which hosts ftp.gromacs.org) got hit hard by the downloads and they throttle (some) connections. Note mine, though, as you can see I got a 28.6 M/s average download speed (but that's of course an unfair comparison). Not sure how to check whether the downloads are really being throttled, but perhaps we should use an alternative host or torrent. -Justin 2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408] Cheers, -- Szilárd On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh harshsingh2...@gmail.com wrote: I know this is a silly question but in the downloads section when I click to download it the new window opens and 0bit tar file is downloaded.I switched to windows but even then the new tab doesn't show anything.I don't understand why is this happening. -- 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. -- 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] obtaining .gro timeframe
Thanks a lot, Justin. It's much clearer, but one last question: If the coordinates in sample.gro extracted from xtc trajectory using trjconv ( without any application of pbc) are unwrapped, why almost all of them happen to lie in the box, as can be seen in the following snapshot? I would expect many of them scattered in space, beyond original box? https://www.dropbox.com/sh/1za0snsw20is106/AADU7hG_CMQmtZ8iI4XGKz-va Dark blue line is the box boundary. Thanks Chetan On Wed, Jul 2, 2014 at 5:14 AM, Justin Lemkul jalem...@vt.edu wrote: On 7/1/14, 11:28 PM, Chetan Mahajan wrote: Thanks, Justin. *Until now, I was thinking that xtc coordinates are wrapped. It's good to know that coordinates from xtc files are unwrapped (please comment if not correct, since we talked only with respect to gro That is correct. mdrun doesn't care about our visualization convenience. No sense in wasting performance doing imaging on the fly when it's not necessary. file). *But I am confused at another thing. I have known at the origin of the box is at one of its vertices ( is that not true?). *Then why are some coordinates in .gro file (the one generated at the end of gromacs MD run) negative, if coordinates are wrapped in the box?* Molecules are made whole; sometimes they're translated in the positive direction, sometimes in the negative direction, depending on how the molecule is being reconstructed. Is my original command using trjconv okay? OK is relative. In this case, you seem troubled by the slight difference in convention, but there's nothing wrong with the command. If you want trjconv to make molecules whole, use -pbc mol or -pbc whole. Your original command simply dumps the coordinates and does nothing about periodicity. Whereas I do get a sample x-coordinate in .gro file, generated at the end of MD run (let's call it gro1) from that in .gro file, generated using trjconv on xtc (let's call it gro2) by adding a box length to concerned coordinate in gro2, (as shown in excerpt 1) , it's only by subtracting a boxlength that we interconvert between similar values, as shown in excerpt 2 of the SAME file. *Why is there no consistency of conversion between SAME two .gro files for all the coordinates? How do I mathematically obtain file 2 from file 1 with some consistent measure? * See above. trjconv will do it for you. -Justin - : for .gro file at the end of gromacs MD run (gro1) + : for .gro timeframe file obtained from .xtc trajectory ( using trjconv) (gro2) *EXCERT 1* - 11SOLHW1 2188 3.244 3.071 10.934 - 11SOLHW2 2189 3.211 2.940 10.842 + 11SOLHW1 2188 0.023 3.071 10.934 + 11SOLHW2 2189 -0.011 2.940 10.842 *EXCERT 2* - 56SOLHW1 2323 -0.031 1.076 1.130 - 56SOLHW2 2324 -0.040 1.096 1.292 + 56SOLHW1 2323 3.191 1.076 1.130 + 56SOLHW2 2324 3.182 1.096 1.292 Thanks Chetan On Tue, Jul 1, 2014 at 8:10 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/1/14, 9:08 PM, Chetan Mahajan wrote: Thanks, Justin. Are you saying, the coordinates in .gro file extracted from xtc trajectory are not wrapped, whereas those in the .gro file generated at the end of gromacs MD run are wrapped in the box? Yes, unless you've manipulated the trajectory in some way with trjconv beforehand. Now I have a question: the negative coordinates that are present in the following text are from .gro file (generated at the end of MD run), whereas positive ones are from .gro file obtained using trjconv on xtc. Either way, it's a periodicity effect. Molecules are made whole. -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. -- == 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
Re: [gmx-users] obtaining .gro timeframe
On 7/2/14, 6:45 PM, Chetan Mahajan wrote: Thanks a lot, Justin. It's much clearer, but one last question: If the coordinates in sample.gro extracted from xtc trajectory using trjconv ( without any application of pbc) are unwrapped, why almost all of them happen to lie in the box, as can be seen in the following snapshot? I would expect many of them scattered in space, beyond original box? https://www.dropbox.com/sh/1za0snsw20is106/AADU7hG_CMQmtZ8iI4XGKz-va Dark blue line is the box boundary. A central unit cell is still maintained; it's just that the molecules aren't necessarily whole. -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 5.0 download
I ran the md5sum but it does not match with any of the hashes.What should I do now? On Wed, Jul 2, 2014 at 5:55 PM, Szilárd Páll pall.szil...@gmail.com wrote: On Wed, Jul 2, 2014 at 11:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/2/14, 4:36 PM, Szilárd Páll wrote: The link is correct, something must be broken on your side. Try using e.g. wget: $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l gromacs*.gz --2014-07-02 22:34:44-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz = `gromacs-5.0.tar.gz' Resolving ftp.gromacs.org... 130.238.41.205 Connecting to ftp.gromacs.org|130.238.41.205|:21... connected. Logging in as anonymous ... Logged in! == SYST ... done.== PWD ... done. == TYPE I ... done. == CWD (1) /pub/gromacs ... done. == SIZE gromacs-5.0.tar.gz ... 26862408 == PASV ... done.== RETR gromacs-5.0.tar.gz ... done. Length: 26862408 (26M) (unauthoritative) 100%[] 26,862,408 28.6M/s in 0.9s I'm having a similar problem as the OP. The web interface just seems to hang and using wget takes over an hour with a download rate of 4 KB/sec. This is true at work (hardwired workstation) and at home (laptop on wifi) OK, that's alarming. Perhaps uu.se (which hosts ftp.gromacs.org) got hit hard by the downloads and they throttle (some) connections. Note mine, though, as you can see I got a 28.6 M/s average download speed (but that's of course an unfair comparison). Not sure how to check whether the downloads are really being throttled, but perhaps we should use an alternative host or torrent. -Justin 2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408] Cheers, -- Szilárd On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh harshsingh2...@gmail.com wrote: I know this is a silly question but in the downloads section when I click to download it the new window opens and 0bit tar file is downloaded.I switched to windows but even then the new tab doesn't show anything.I don't understand why is this happening. -- 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. -- 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. -- Harshkumar Singh 2nd Year Integrated MSc Chemistry IIT Bombay. -- 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] Solvating protein in a CG representation - genbox problem
Dear gromacs users, I’m following this tutorial - http://md.chem.rug.nl/cgmartini/index.php/proteins in order to performed a CG simulation of an specific protein in a water box. My problem is that when i’m trying to solvate my protein with genbox, by using the next command: genbox -cp COR15A_CG-box.gro -cs water-box-303K-1bar.gro -vdwd 0.21 -o COR15A_CG-solvated.gro The water box is placed next to the protein instead of surrounding it- http://cl.ly/1U2F1H3y3n2w. I used the following command to center my protein before i used genbox, without luck :/ editconf -f COR15A_CG.pdb -center 0 0 0 -o COR15A_CG-box.gro -c -d 2.0 -bt cubic I’m just start by using a CG representation of biological systems, so any help will be welcome. Have a nice day, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile Teléfono: 56-71-201 798, Fax: 56-71-201 561 Email: carlos.navarr...@gmail.com or cnava...@utalca.cl -- 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 5.0 download
On Wed, Jul 2, 2014 at 6:55 PM, Harshkumar Singh harshsingh2...@gmail.com wrote: I ran the md5sum but it does not match with any of the hashes.What should I do now? Which file from which server (/which URL) did you download? What md5 did you get? Roland On Wed, Jul 2, 2014 at 5:55 PM, Szilárd Páll pall.szil...@gmail.com wrote: On Wed, Jul 2, 2014 at 11:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/2/14, 4:36 PM, Szilárd Páll wrote: The link is correct, something must be broken on your side. Try using e.g. wget: $ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l gromacs*.gz --2014-07-02 22:34:44-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz = `gromacs-5.0.tar.gz' Resolving ftp.gromacs.org... 130.238.41.205 Connecting to ftp.gromacs.org|130.238.41.205|:21... connected. Logging in as anonymous ... Logged in! == SYST ... done.== PWD ... done. == TYPE I ... done. == CWD (1) /pub/gromacs ... done. == SIZE gromacs-5.0.tar.gz ... 26862408 == PASV ... done.== RETR gromacs-5.0.tar.gz ... done. Length: 26862408 (26M) (unauthoritative) 100%[] 26,862,408 28.6M/s in 0.9s I'm having a similar problem as the OP. The web interface just seems to hang and using wget takes over an hour with a download rate of 4 KB/sec. This is true at work (hardwired workstation) and at home (laptop on wifi) OK, that's alarming. Perhaps uu.se (which hosts ftp.gromacs.org) got hit hard by the downloads and they throttle (some) connections. Note mine, though, as you can see I got a 28.6 M/s average download speed (but that's of course an unfair comparison). Not sure how to check whether the downloads are really being throttled, but perhaps we should use an alternative host or torrent. -Justin 2014-07-02 22:34:45 (28.6 MB/s) - `gromacs-5.0.tar.gz' saved [26862408] Cheers, -- Szilárd On Wed, Jul 2, 2014 at 8:48 PM, Harshkumar Singh harshsingh2...@gmail.com wrote: I know this is a silly question but in the downloads section when I click to download it the new window opens and 0bit tar file is downloaded.I switched to windows but even then the new tab doesn't show anything.I don't understand why is this happening. -- 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. -- 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. -- Harshkumar Singh 2nd Year Integrated MSc Chemistry IIT Bombay. -- 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. -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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] Solvating protein in a CG representation - genbox roblem
Never mind. I used editconf before the energy-minimisation on vacuum (specifying the size-box) and now, when i used genbox on the ’new’ structured it worked :D -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile Teléfono: 56-71-201 798, Fax: 56-71-201 561 Email: carlos.navarr...@gmail.com or cnava...@utalca.cl On Wednesday, July 2, 2014 at 8:56 PM, Carlos Navarrro Retamal wrote: Dear gromacs users, I’m following this tutorial - http://md.chem.rug.nl/cgmartini/index.php/proteins in order to performed a CG simulation of an specific protein in a water box. My problem is that when i’m trying to solvate my protein with genbox, by using the next command: genbox -cp COR15A_CG-box.gro -cs water-box-303K-1bar.gro -vdwd 0.21 -o COR15A_CG-solvated.gro The water box is placed next to the protein instead of surrounding it- http://cl.ly/1U2F1H3y3n2w. I used the following command to center my protein before i used genbox, without luck :/ editconf -f COR15A_CG.pdb -center 0 0 0 -o COR15A_CG-box.gro -c -d 2.0 -bt cubic I’m just start by using a CG representation of biological systems, so any help will be welcome. Have a nice day, Carlos -- Carlos Navarro Retamal Bioinformatic engineer Ph.D(c) in Applied Science, Universidad de Talca, Chile Center of Bioinformatics and Molecular Simulations (CBSM) Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile Teléfono: 56-71-201 798, Fax: 56-71-201 561 Email: carlos.navarr...@gmail.com (mailto:carlos.navarr...@gmail.com) or cnava...@utalca.cl (mailto:cnava...@utalca.cl) -- 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 (mailto:gmx-users-requ...@gromacs.org). -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] regarding error during EM
*Fatal error:* 25 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This usually means that your system is not well equilibrated. -- 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] Graphene topology file
Dear Justin, Thanks for the reply but I am writing the .n2t file still getting the error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. What should I do? Moreover i don't think that n2t file tells program to use graphite_oplsaa force field. Regards Sukriti Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Wednesday, July 2, 2014 11:29 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote: Dear all, I want to simulate graphite in water, for which i am trying to create a topology file for graphite. As its .rtp file cannot be written correctly, i tried to use g_x2top command following the steps given in following tutorial. http://chembytes.wikidot.com/grocnt But I think this tutorial is quite old and hence suitable for older version of gromacs as it still uses FF.dat file. Moreover if i am trying to make a new forcefield directory with name graphite_oplsaa containing the modified files like .n2t,.rtp and .itp, its giving me an error that Could not find force field 'graphite_oplsaa' in current directory, install tree or GMXDATA path. When I try to add this forcefield in original path ie. user/share/gromacs/top, it does not allow me to do that as i am not the administrator. Can anyone please let me know how to create the topology file. I require 3 graphene sheets with pbc. I have created the .pdb file using nanobuilder in vmd. The tutorial is indeed outdated but the logic is fairly sound. You don't have to modify anything in $GMXLIB (system-wide); you can just create an .n2t file in the working directory and it will override the one at the force field level. -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. -- 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] conf.gro
hello gromacs users i am working on protein ligand compex with popc membrane for ligand prepration from where i can get conf.gro file because i am using conf.gro file from gromacs folder (tutor folder -water ) gromacs 4.5.7. kindly help -- 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.
