Re: [gmx-users] first residue in chains warning issue
Dear Justin, Is there any significant difference between the equilibrated states of the protein equilibrated by NPT with all-bonds constrained and without any constraints? If the difference is quite small, then I can choose constraining bonds to increase time step. Thanks a lot. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Monday, 18 May 2015 9:44 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] first residue in chains warning issue On 5/18/15 7:39 AM, Ming Tang wrote: Dear Justin, After minimization, I got the following note when using NPT. NOTE 1 [file topol.top, line 49]: The bond in molecule-type Protein_chain_A between atoms 1 N and 2 H1 has an estimated oscillational period of 1.0e-02 ps, which is less than 10 times the time step of 1.0e-03 ps. Maybe you forgot to change the constraints mdp option. Does this has something to do with the warning given by pdb2gmx? When reducing dt from 0.001ps to 0.0009ps, the note is gone. Is there anything wrong with my topol.top? No, as the note says, you probably aren't using constraints, which if you want a 1-fs or larger value of dt, you need to be using. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] LINSC WARNING
Dear Gromacs Users, When I run npt equilibrium, I set the step size is 4fs. I go many LINCS WARNING bonds that rotate more than 30 degrees When I reduce the step size to 2fs. All thing is fine. Could someone here explain to me? Finally, I want to use step size is 4fs. Any suggestions for me? Thank you Tuong Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] How can i install DSSP for gromacs on centos6?
Hi there I tried to execute dssp for gromacs 4.5.7 by following this instruction: #sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 https://www.researchgate.net/go.Deref.html?url=ftp%3A%2F%2Fftp.cmbi.ru.nl%2Fpub%2Fsoftware%2Fdssp%2Fdssp-2.0.4-linux-amd64 -O /usr/local/bin/dssp #sudo chmod a+x /usr/local/bin/dssp #export DSSP=/usr/local/bin/dssp then I run g_do_dssp and I got this error: - Program g_do_dssp, VERSION 4.5.7 Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/tools/do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddKnNFex ddYd8PhB /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FErrors --- It also makes some files like ddYd8PhB! I have tried two different binary file but it didn't work. In addition there is a binary g_do_dssp from gromacs package . How can I point it to export dssp? plz help me to fix that problem -- Homa Ahmadi Shahed University Faculty of Basic Sciences Alternative email h.ahm...@shahed.ac.ir h.ahm...@ast.ui.ac.ir -- 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] H-bonding
Hello all, I am trying to see what happens to the no. of Watson-Crick hydrogen bonds between two parallel chains of a double stranded DNA on incorporating a flat graphene sheet. The no of interchain H-bonds are supposed to decrease with time. But I am not sure how to use g_hbond in order to demonstrate this. How should I make index groups for the two chains of DNA? Should I take all the atoms into account (except backbone) and then index them like chain_A and chain_B and then analyze the hbnum.xvg file from g_hbond? Your help is required. Soumadwip Research Fellow IITB 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] water box moves during MD simulation
Dear Mark, Thanks a lot. Is it possible to get the water box fixed through command in .mdp, or using a specific option to fix the water box, like -nojump for g_traj? -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: Wednesday, 20 May 2015 7:31 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] water box moves during MD simulation Hi, You can add (say) -1.23 to every x coordinate and you have a description of the same system. So you can pick any of these for doing the simulation, and any of these for representing the trajectory afterwards. Mark On Wed, May 20, 2015 at 11:19 AM Ming Tang m21.t...@qut.edu.au wrote: Dear Brother， What does Mark mean？ Sent from my Huawei Mobile Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Nothing wrong with the .mdp file. But you should check your assumption that there's a single meaningful location where an infinite periodic system should be located :-) There's lots of equivalent representations, so mdrun suits itself. Mark On Wed, May 20, 2015 at 9:05 AM Ming Tang m21.t...@qut.edu.au wrote: Dear all, After MD dynamic simulation for 100 ps, I found the water box was moving during the simulation, but my protein was inside the water box all the time. Here is the . mdp file I used: integrator = md dt = 0.001 nsteps = 10 nstxout = 1000 nstvout = 1000 nstlog = 1000 nstxout-compressed= 100 xtc-precision= 10 cutoff-scheme=verlet rlist= 1.4 coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_r= 15 vdw-modifier = potential-switch rvdw-switch = 0.8 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein non-protein tau-t= 1.0 1.0 ref-t= 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau-p= 12.0 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all pbc = xyz constraints = h-bonds Could anybody tell me what's wrong with my .mdp file? Thanks in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] Pull code
On 5/22/15 7:00 AM, Ming Tang wrote: Dear Justin, I want to simulate my triple helix using SMD, Can I use umbrella + distance? Shrug. Depends on what you're doing and trying to observe. I saw many people doing SMD simulation by fixing one end and pull another end in their journal. Besides, my triple helix deviates a bit from Z axis, but I do not know the angle. I checked both dim for distance and pull-vec for direction, and found both of them needs pull direction. If I set dim = N N Y, will the force-deformation be reliable? Align with x using editconf -princ, then rotate to your heart's desire with editconf -rotate to align with whatever axis you want. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Editconf error
On 5/22/15 4:57 PM, Jorge Dagnino wrote: As this is my first time with this kind of error, i don't know which part of the coordinate file is relevant, :( If you can tell me which part do you need, i can paste it Email me the files off-list. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Editconf error
On 5/22/15 4:07 PM, Jorge Dagnino wrote: Here are the complete files. pdb2gmx input: http://pastebin.com/HBmrR0eF .gro output: http://paste2.org/ahY6MB99 editconf input: http://paste2.org/9fPp6J02 editconf output: http://paste2.org/v1IsPp6O Can you just upload all the relevant coordinate files so I don't have to copy-paste tens of thousands of lines of text? :) -Justin Thanks. 2015-05-22 16:21 GMT-03:00 Barnett, James W jbarn...@tulane.edu: It'd be more helpful for troubleshooting your problem if you post the entire file in each case, not just parts of them. If it's a large file use Pastebin.com or something similar. -- James Wes Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu LinkedIn From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Jorge Dagnino jdagn...@gmail.com Sent: Friday, May 22, 2015 11:06 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Editconf error Here are the coordinates from my pdb file: ATOM 1 N MET G 27 69.331 43.147 76.443 1.00 0.00 N ATOM 2 CA MET G 27 68.996 44.047 75.331 1.00 0.00 C ATOM 3 C MET G 27 67.818 43.550 74.510 1.00 0.00 C ATOM 4 O MET G 27 66.981 44.264 73.969 1.00 0.00 O ATOM 5 CB MET G 27 70.152 44.201 74.325 1.00 0.00 C ATOM 6 CG MET G 27 70.024 45.547 73.614 1.00 0.00 C ATOM 7 SD MET G 27 70.710 46.841 74.678 1.00 0.00 S ATOM 8 CE MET G 27 70.252 48.118 73.481 1.00 0.00 C ATOM 9 N ALA G 28 67.504 42.250 74.523 1.00 0.00 N ATOM 10 CA ALA G 28 66.247 41.666 74.095 1.00 0.00 C ATOM 11 C ALA G 28 64.968 42.391 74.469 1.00 0.00 C ATOM 12 O ALA G 28 64.064 42.543 73.651 1.00 0.00 O ATOM 13 CB ALA G 28 66.323 40.167 74.396 1.00 0.00 C ATOM 14 N GLU G 29 64.839 42.732 75.756 1.00 0.00 N ATOM 15 CA GLU G 29 63.656 43.315 76.334 1.00 0.00 C ATOM 16 C GLU G 29 63.567 44.789 75.955 1.00 0.00 C ATOM 17 O GLU G 29 62.480 45.354 75.850 1.00 0.00 O ATOM 18 CB GLU G 29 63.662 43.143 77.854 1.00 0.00 C ATOM 19 CG GLU G 29 64.822 43.835 78.553 1.00 0.00 C ATOM 20 CD GLU G 29 64.794 43.644 80.055 1.00 0.00 C ATOM 21 OE1 GLU G 29 63.801 44.058 80.689 1.00 0.00 O ATOM 22 OE2 GLU G 29 65.765 43.078 80.601 1.00 0.00 O1- And here are the coordinates from the .gro file Giant Rising Ordinary Mutants for A Clerical Setup 16231 27MET N1 6.933 4.315 7.644 27MET H12 7.011 4.352 7.695 27MET H23 6.854 4.307 7.705 27MET H34 6.957 4.224 7.608 27MET CA5 6.900 4.405 7.533 27MET HA6 6.878 4.489 7.582 27MET CB7 7.015 4.420 7.432 27METHB18 7.103 4.416 7.481 27METHB29 7.011 4.346 7.365 27MET CG 10 7.002 4.555 7.361 27METHG1 11 7.052 4.545 7.275 27METHG2 12 6.905 4.567 7.343 27MET SD 13 7.071 4.684 7.468 27MET CE 14 7.025 4.812 7.348 27METHE1 15 7.053 4.901 7.383 27METHE2 16 7.071 4.794 7.261 27METHE3 17 6.926 4.811 7.334 27MET C 18 6.782 4.355 7.451 27MET O 19 6.698 4.426 7.397 28ALA N 20 6.750 4.225 7.452 28ALA H 21 6.820 4.162 7.486 28ALA CA 22 6.625 4.167 7.410 28ALA HA 23 6.620 4.184 7.311 28ALA CB 24 6.632 4.017 7.440 28ALAHB1 25 6.547 3.973 7.411 28ALAHB2 26 6.709 3.976 7.389 28ALAHB3 27 6.646 4.003 7.538 28ALA C 28 6.497 4.239 7.447 28ALA O 29 6.406 4.254 7.365 29GLU N 30 6.484 4.273 7.576 29GLU H 31 6.562 4.257 7.636 29GLU CA 32 6.366 4.332 7.633 29GLU HA 33 6.289 4.281 7.594 29GLU CB 34 6.366 4.314 7.785 29GLUHB1 35 6.281 4.352 7.822 29GLUHB2 36 6.371 4.217 7.806 29GLU CG 37 6.482 4.384 7.855 29GLUHG1 38 6.568 4.346 7.820 29GLUHG2 39 6.478 4.481 7.836 29GLU CD 40 6.479 4.364 8.005 29GLUOE1 41 6.380 4.406 8.069 29GLUOE2 42 6.576 4.308 8.060 29GLU C 43 6.357 4.479 7.595 29GLU O 44 6.248 4.535 7.585 and this is the output from editconf. Giant Rising Ordinary Mutants for A Clerical
Re: [gmx-users] conserved energy
On 5/22/15 11:56 AM, Ahmet Yıldırım wrote: Dear users, The total energy obtained from the .edr file is the sum of potential and kinetic energy of system. But there is not any information about conserved energy in manual. Maybe I couldn't find it. I am looking for answers of the following questions: -Which energy contributions/terms does the conserved energy include? -How I get individual contributions (like constrains' contribution) to the conserved energy? http://lmgtfy.com/?q=gromacs+%22conserved+energy%22+site%3Amailman-1.sys.kth.se :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Editconf error
Here are the complete files. pdb2gmx input: http://pastebin.com/HBmrR0eF .gro output: http://paste2.org/ahY6MB99 editconf input: http://paste2.org/9fPp6J02 editconf output: http://paste2.org/v1IsPp6O Thanks. 2015-05-22 16:21 GMT-03:00 Barnett, James W jbarn...@tulane.edu: It'd be more helpful for troubleshooting your problem if you post the entire file in each case, not just parts of them. If it's a large file use Pastebin.com or something similar. -- James Wes Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu LinkedIn From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Jorge Dagnino jdagn...@gmail.com Sent: Friday, May 22, 2015 11:06 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Editconf error Here are the coordinates from my pdb file: ATOM 1 N MET G 27 69.331 43.147 76.443 1.00 0.00 N ATOM 2 CA MET G 27 68.996 44.047 75.331 1.00 0.00 C ATOM 3 C MET G 27 67.818 43.550 74.510 1.00 0.00 C ATOM 4 O MET G 27 66.981 44.264 73.969 1.00 0.00 O ATOM 5 CB MET G 27 70.152 44.201 74.325 1.00 0.00 C ATOM 6 CG MET G 27 70.024 45.547 73.614 1.00 0.00 C ATOM 7 SD MET G 27 70.710 46.841 74.678 1.00 0.00 S ATOM 8 CE MET G 27 70.252 48.118 73.481 1.00 0.00 C ATOM 9 N ALA G 28 67.504 42.250 74.523 1.00 0.00 N ATOM 10 CA ALA G 28 66.247 41.666 74.095 1.00 0.00 C ATOM 11 C ALA G 28 64.968 42.391 74.469 1.00 0.00 C ATOM 12 O ALA G 28 64.064 42.543 73.651 1.00 0.00 O ATOM 13 CB ALA G 28 66.323 40.167 74.396 1.00 0.00 C ATOM 14 N GLU G 29 64.839 42.732 75.756 1.00 0.00 N ATOM 15 CA GLU G 29 63.656 43.315 76.334 1.00 0.00 C ATOM 16 C GLU G 29 63.567 44.789 75.955 1.00 0.00 C ATOM 17 O GLU G 29 62.480 45.354 75.850 1.00 0.00 O ATOM 18 CB GLU G 29 63.662 43.143 77.854 1.00 0.00 C ATOM 19 CG GLU G 29 64.822 43.835 78.553 1.00 0.00 C ATOM 20 CD GLU G 29 64.794 43.644 80.055 1.00 0.00 C ATOM 21 OE1 GLU G 29 63.801 44.058 80.689 1.00 0.00 O ATOM 22 OE2 GLU G 29 65.765 43.078 80.601 1.00 0.00 O1- And here are the coordinates from the .gro file Giant Rising Ordinary Mutants for A Clerical Setup 16231 27MET N1 6.933 4.315 7.644 27MET H12 7.011 4.352 7.695 27MET H23 6.854 4.307 7.705 27MET H34 6.957 4.224 7.608 27MET CA5 6.900 4.405 7.533 27MET HA6 6.878 4.489 7.582 27MET CB7 7.015 4.420 7.432 27METHB18 7.103 4.416 7.481 27METHB29 7.011 4.346 7.365 27MET CG 10 7.002 4.555 7.361 27METHG1 11 7.052 4.545 7.275 27METHG2 12 6.905 4.567 7.343 27MET SD 13 7.071 4.684 7.468 27MET CE 14 7.025 4.812 7.348 27METHE1 15 7.053 4.901 7.383 27METHE2 16 7.071 4.794 7.261 27METHE3 17 6.926 4.811 7.334 27MET C 18 6.782 4.355 7.451 27MET O 19 6.698 4.426 7.397 28ALA N 20 6.750 4.225 7.452 28ALA H 21 6.820 4.162 7.486 28ALA CA 22 6.625 4.167 7.410 28ALA HA 23 6.620 4.184 7.311 28ALA CB 24 6.632 4.017 7.440 28ALAHB1 25 6.547 3.973 7.411 28ALAHB2 26 6.709 3.976 7.389 28ALAHB3 27 6.646 4.003 7.538 28ALA C 28 6.497 4.239 7.447 28ALA O 29 6.406 4.254 7.365 29GLU N 30 6.484 4.273 7.576 29GLU H 31 6.562 4.257 7.636 29GLU CA 32 6.366 4.332 7.633 29GLU HA 33 6.289 4.281 7.594 29GLU CB 34 6.366 4.314 7.785 29GLUHB1 35 6.281 4.352 7.822 29GLUHB2 36 6.371 4.217 7.806 29GLU CG 37 6.482 4.384 7.855 29GLUHG1 38 6.568 4.346 7.820 29GLUHG2 39 6.478 4.481 7.836 29GLU CD 40 6.479 4.364 8.005 29GLUOE1 41 6.380 4.406 8.069 29GLUOE2 42 6.576 4.308 8.060 29GLU C 43 6.357 4.479 7.595 29GLU O 44 6.248 4.535 7.585 and this is the output from editconf. Giant Rising Ordinary Mutants for A Clerical Setup 16231 27MET N1-nan-nan-nan 27MET H12-nan-nan-nan 27MET H23-nan
Re: [gmx-users] PMF calculation with constraint distance
On 5/21/15 5:19 PM, leila salimi wrote: Thanks Justin. Yes I have done PMF with Blue moon ensemble with DFT. Now I want to do the same with gromacs to have some knowledge about my FF parameters and compare with my DFT results! You meant I have to do with different configuration and average the forces? I am wondering that I did in DFT for each constrained distances around 15 ps MD and then I used averaged forces for each distances! I don't know what your QM involved; when I hear Blue moon I think of the beverage - cheers! :) If your QM gave you an energy vs. time plot, that's not a PMF. That's a potential energy scan with some fixed intermolecular geometry. Again, maybe I just don't know what you're doing. In principle you could do the same thing with a rigid constraint between the groups, but your post is a bit confusing. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] first residue in chains warning issue
On 5/22/15 3:39 AM, Ming Tang wrote: Dear Justin, Is there any significant difference between the equilibrated states of the protein equilibrated by NPT with all-bonds constrained and without any constraints? If the difference is quite small, then I can choose constraining bonds to increase time step. This is generally (read: pretty much always) what people do in biomolecular simulations. The bonds are rarely (read: practically never) excited from their ground state, so constraints are a reasonable approximation. This isn't universal, but it's definitely true in most biological systems at ambient conditions. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Editconf error
As this is my first time with this kind of error, i don't know which part of the coordinate file is relevant, :( If you can tell me which part do you need, i can paste it Thanks. 2015-05-22 17:17 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 5/22/15 4:07 PM, Jorge Dagnino wrote: Here are the complete files. pdb2gmx input: http://pastebin.com/HBmrR0eF .gro output: http://paste2.org/ahY6MB99 editconf input: http://paste2.org/9fPp6J02 editconf output: http://paste2.org/v1IsPp6O Can you just upload all the relevant coordinate files so I don't have to copy-paste tens of thousands of lines of text? :) -Justin Thanks. 2015-05-22 16:21 GMT-03:00 Barnett, James W jbarn...@tulane.edu: It'd be more helpful for troubleshooting your problem if you post the entire file in each case, not just parts of them. If it's a large file use Pastebin.com or something similar. -- James Wes Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu LinkedIn From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Jorge Dagnino jdagn...@gmail.com Sent: Friday, May 22, 2015 11:06 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Editconf error Here are the coordinates from my pdb file: ATOM 1 N MET G 27 69.331 43.147 76.443 1.00 0.00 N ATOM 2 CA MET G 27 68.996 44.047 75.331 1.00 0.00 C ATOM 3 C MET G 27 67.818 43.550 74.510 1.00 0.00 C ATOM 4 O MET G 27 66.981 44.264 73.969 1.00 0.00 O ATOM 5 CB MET G 27 70.152 44.201 74.325 1.00 0.00 C ATOM 6 CG MET G 27 70.024 45.547 73.614 1.00 0.00 C ATOM 7 SD MET G 27 70.710 46.841 74.678 1.00 0.00 S ATOM 8 CE MET G 27 70.252 48.118 73.481 1.00 0.00 C ATOM 9 N ALA G 28 67.504 42.250 74.523 1.00 0.00 N ATOM 10 CA ALA G 28 66.247 41.666 74.095 1.00 0.00 C ATOM 11 C ALA G 28 64.968 42.391 74.469 1.00 0.00 C ATOM 12 O ALA G 28 64.064 42.543 73.651 1.00 0.00 O ATOM 13 CB ALA G 28 66.323 40.167 74.396 1.00 0.00 C ATOM 14 N GLU G 29 64.839 42.732 75.756 1.00 0.00 N ATOM 15 CA GLU G 29 63.656 43.315 76.334 1.00 0.00 C ATOM 16 C GLU G 29 63.567 44.789 75.955 1.00 0.00 C ATOM 17 O GLU G 29 62.480 45.354 75.850 1.00 0.00 O ATOM 18 CB GLU G 29 63.662 43.143 77.854 1.00 0.00 C ATOM 19 CG GLU G 29 64.822 43.835 78.553 1.00 0.00 C ATOM 20 CD GLU G 29 64.794 43.644 80.055 1.00 0.00 C ATOM 21 OE1 GLU G 29 63.801 44.058 80.689 1.00 0.00 O ATOM 22 OE2 GLU G 29 65.765 43.078 80.601 1.00 0.00 O1- And here are the coordinates from the .gro file Giant Rising Ordinary Mutants for A Clerical Setup 16231 27MET N1 6.933 4.315 7.644 27MET H12 7.011 4.352 7.695 27MET H23 6.854 4.307 7.705 27MET H34 6.957 4.224 7.608 27MET CA5 6.900 4.405 7.533 27MET HA6 6.878 4.489 7.582 27MET CB7 7.015 4.420 7.432 27METHB18 7.103 4.416 7.481 27METHB29 7.011 4.346 7.365 27MET CG 10 7.002 4.555 7.361 27METHG1 11 7.052 4.545 7.275 27METHG2 12 6.905 4.567 7.343 27MET SD 13 7.071 4.684 7.468 27MET CE 14 7.025 4.812 7.348 27METHE1 15 7.053 4.901 7.383 27METHE2 16 7.071 4.794 7.261 27METHE3 17 6.926 4.811 7.334 27MET C 18 6.782 4.355 7.451 27MET O 19 6.698 4.426 7.397 28ALA N 20 6.750 4.225 7.452 28ALA H 21 6.820 4.162 7.486 28ALA CA 22 6.625 4.167 7.410 28ALA HA 23 6.620 4.184 7.311 28ALA CB 24 6.632 4.017 7.440 28ALAHB1 25 6.547 3.973 7.411 28ALAHB2 26 6.709 3.976 7.389 28ALAHB3 27 6.646 4.003 7.538 28ALA C 28 6.497 4.239 7.447 28ALA O 29 6.406 4.254 7.365 29GLU N 30 6.484 4.273 7.576 29GLU H 31 6.562 4.257 7.636 29GLU CA 32 6.366 4.332 7.633 29GLU HA 33 6.289 4.281 7.594 29GLU CB 34 6.366 4.314 7.785 29GLUHB1 35 6.281 4.352 7.822 29GLUHB2 36 6.371 4.217 7.806 29GLU CG 37 6.482 4.384 7.855 29GLUHG1 38 6.568 4.346 7.820
Re: [gmx-users] H-bond query
On 5/22/15 9:19 AM, soumadwip ghosh wrote: Hello all, I am trying to see what happens to the no. of Watson-Crick hydrogen bonds between two parallel chains of a double stranded DNA on incorporating a flat graphene sheet. The no of interchain H-bonds are supposed to decrease with time. But I am not sure how to use g_hbond in order to demonstrate this. How should I make index groups for the two chains of DNA? Should I take all the atoms into account (except backbone) and then index them like chain_A and chain_B and then analyze the hbnum.xvg file from g_hbond? Furthermore, in the hbnum.xvg file the third column represents the no. of H-bond within the distance cut-off and the 2nd one is the total no of hydrogen bonds as a function of simulation time. So, which one should I plot in this case against time? You probably care about the actual H-bonds, not the atom pairs that are within distance but don't satisfy the angle criterion. Watson-Crick hydrogen bonding is a very straightforward definition; the index group should be straightforward. For anything else that comes up in a melted state, well, that's up to what you're seeing and what you're interested in. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] conserved energy
You should also understand energy at the atomic level, the standard atom-atom inteeractions from general O chem, or chem suck as leonard jones and coulumb...per the standard, non-indexed outputs...they do not follow newtonian based energy systems even though the algorithm is newtonian based in most aspects, which I personally find a miss statement, but was shown to me years ago as true because it essentially treats everything as a moving billiard, then adds the other factors aftwerwards through intigration at set points...using tables which again I am amazed work as they are essentially from the CRC chem book, or standard books prior to computers and very small as far as input overall...pardon my spelling...and redundancy... also for anyone with a pesudonym from Oregon state university...not pertaining to myself...as I post here, mit dieses email nicht zu oft... Stephan Watkins, PhD Gesendet:Freitag, 22. Mai 2015 um 22:19 Uhr Von:Justin Lemkul jalem...@vt.edu An:gmx-us...@gromacs.org Betreff:Re: [gmx-users] conserved energy On 5/22/15 11:56 AM, Ahmet Yldrm wrote: Dear users, The total energy obtained from the .edr file is the sum of potential and kinetic energy of system. But there is not any information about conserved energy in manual. Maybe I couldnt find it. I am looking for answers of the following questions: -Which energy contributions/terms does the conserved energy include? -How I get individual contributions (like constrains contribution) to the conserved energy? http://lmgtfy.com/?q=gromacs+%22conserved+energy%22+site%3Amailman-1.sys.kth.se :) -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Cant 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] LINSC WARNING
On 5/22/15 10:46 AM, Ahmet Yıldırım wrote: I haven't tried vsites on GPU. I just used them for the united atom ffs (espically GROMOS ffs) with reaction field method. Actually I didn't get good results about the ligand in the system. Maybe the problem was force field (54A7) I used. Because for GROMOS ffs there is another problem that is helix melting :). If helices are falling apart in 54A7, something else is going on. 53A6 has known deficiencies there, but they were fixed in 54A7. Might even be too stable. -Justin 2015-05-22 16:08 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: Hi, On Fri, May 22, 2015 at 3:57 PM Albert mailmd2...@gmail.com wrote: that's interesting. How about the ligand in the system? The hydrogen should also be treated in virtual site? Is it possible treat the binding pocket as explicit atoms, and all the rest in virtual hydrogen? You're probably thinking of united atoms, which are entirely distinct. You can read all about virtual sites in the manual and publications ;-) Does it support GPU? Yes Mark thx a lot Albert On 05/22/2015 03:51 PM, Ahmet Yıldırım wrote: Hi Phan, If you want to use the time step of 4 fs, you can try to use virtual sites (gmx pdb2gmx -f ... -vsite hydrogens). Please look at the following web site. https://www.wenmr.eu/wenmr/md-simulations-using-gromacs-web-server Virtual sites:The use of virtual sites offers another possibility to increase the efficiency of the simulation. These are used to replace hydrogen atoms, removing the fastest vibrations in the system that otherwise limit the time step that can be used. Simulations run with virtual sites can therefore use a time step of 4 fs, instead of the 2 fs that is used for simulations with explicit hydrogen atoms -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Lincs all-bonds causing instability in otherwise stable system
Hi, After further thought, the base problem is that there must be at least one rigid triangle, and LINCS can't do this because it couples constraints too much. The water models use [settles] to solve the particular case of a single triangle, and TIP4P and TIP5P water models are implemented with virtual sites on such a triangle. So with a bit of pencil and paper, I'm sure you could e.g. have a Me-Me-O rigid triangle and use a 3out virtual site (see manual) for the sulfur. But you'd only do this if the need to use SHAKE was hurting your simulation performance. Mark On Thu, May 21, 2015 at 10:16 AM Cara Kreck cara.kr...@student.curtin.edu.au wrote: Thanks Mark, A grompp warning about problematic constraints sounds like a good idea. DMSO is actually tetrahedral, not planar. Is that possible (and hopefully straightforward) to do with virtual sites? If it is, is there an example I could look at? Thanks, Cara From: mark.j.abra...@gmail.com Date: Wed, 20 May 2015 11:47:43 + To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Lincs all-bonds causing instability in otherwise stable system Hi, Sorry that was so painful for you. The LINCS documentation in the manual suggests that that combination of bonds becoming constraints won't work well. Perhaps we should add a 3-edge cycle detector to grompp? If you actually want a rigid planar DMSO, then three real atoms and a virtual site would be the best implementation. Mark On Wed, May 20, 2015 at 6:41 AM Cara Kreck cara.kr...@student.curtin.edu.au wrote: Hi everyone, I never got a reply to my message but I figured out the problem by myself. Just in case anyone else runs into a similar problem I thought I should explain what was wrong and share the solution. I was using a DMSO topology from the ATB that uses extra bonds to fix the geometry instead of angle or dihedral terms: [ moleculetype ] ; Name nrexcl DMSO 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 SDmso1DMSO S10.128 32.0600 2 ODmso1DMSO O1 -0.448 15.9994 3 CDmso1DMSO C10.160 15.0350 4 CDmso1DMSO C10.160 15.0350 ; 0.000 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 122 0.1530 8.0400e+06 132 0.1938 4.9500e+06 142 0.1938 4.9500e+06 232 0.2794 2.3900e+06 242 0.2794 2.3900e+06 342 0.2912 2.1900e+06 This topology is fine to use with SHAKE but LINCS doesn't seem to be able to handle it. When I removed the extra bonds my simulations were able to run with all bonds constrained by LINCS. Then I found appropriate angle and dihedral parameters in the GROMOS ffbonded.itp file to control the geometry again. My topology file now looks like this: [ moleculetype ] ; Name nrexcl DMSO 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 SDmso1DMSO S10.128 32.0600 2 ODmso1DMSO O1 -0.448 15.9994 3 CDmso1DMSO C10.160 15.0350 4 CDmso1DMSO C10.160 15.0350 ; 0.000 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 122 0.1530 8.0400e+06 132 0.1938 4.9500e+06 142 0.1938 4.9500e+06 [ angles ] ; ai aj ak funct angle fc 314297.40 469.00 3122 106.75 503.00 4122 106.75 503.00 [ dihedrals ] ; GROMOS improper dihedrals ; ai aj ak al funct angle fc 13422 35.26439 334.84617 ; tetrahedral centre I ran an energy minimisation of a single molecule with the new topology and its geometry overlapped the old one perfectly. So the problem was difficult to diagnose but easy to fix. Especially since I was able to energy minimise the individual molecules with all bonds constrained but the constraints went haywire when everything was combined in the full system. Hopefully I can at least save someone else from wasting 3 weeks trying to get a similar topology to work with LINCS. Cara From: cara.kr...@student.curtin.edu.au To: gromacs.org_gmx-users@maillist.sys.kth.se Date: Fri, 15 May 2015 14:31:16 +0800 Subject: [gmx-users] Lincs all-bonds causing instability in otherwise stable system I forgot to include an example of my mdp files. I've tried varying the timestep, running with and without pressure coupling, and obviously changing the constraints as outlined in the previous message:
[gmx-users] How to connect different parts of a polymer?
Dear GMX users I am trying to parametrize GROMOS FF for PAMAM dendrimers. I have paramerized core of the dendrimer, its repeat units, and terminal groups separately. but I dont know how to connect them to build a complete dendrimer so that GROMACS can recognize dendrimer structure exactly. Could you help me, please? Truly yours, Farideh -- 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] water box moves during MD simulation
Hi, You can follow the advice here for making the visual representation whatever you want. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions Mark On Fri, May 22, 2015 at 10:16 AM Ming Tang m21.t...@qut.edu.au wrote: Dear Mark, Thanks a lot. Is it possible to get the water box fixed through command in .mdp, or using a specific option to fix the water box, like -nojump for g_traj? -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto: gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark Abraham Sent: Wednesday, 20 May 2015 7:31 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] water box moves during MD simulation Hi, You can add (say) -1.23 to every x coordinate and you have a description of the same system. So you can pick any of these for doing the simulation, and any of these for representing the trajectory afterwards. Mark On Wed, May 20, 2015 at 11:19 AM Ming Tang m21.t...@qut.edu.au wrote: Dear Brother， What does Mark mean？ Sent from my Huawei Mobile Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Nothing wrong with the .mdp file. But you should check your assumption that there's a single meaningful location where an infinite periodic system should be located :-) There's lots of equivalent representations, so mdrun suits itself. Mark On Wed, May 20, 2015 at 9:05 AM Ming Tang m21.t...@qut.edu.au wrote: Dear all, After MD dynamic simulation for 100 ps, I found the water box was moving during the simulation, but my protein was inside the water box all the time. Here is the . mdp file I used: integrator = md dt = 0.001 nsteps = 10 nstxout = 1000 nstvout = 1000 nstlog = 1000 nstxout-compressed= 100 xtc-precision= 10 cutoff-scheme=verlet rlist= 1.4 coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_r= 15 vdw-modifier = potential-switch rvdw-switch = 0.8 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein non-protein tau-t= 1.0 1.0 ref-t= 300 300 Pcoupl = parrinello-rahman Pcoupltype = isotropic tau-p= 12.0 compressibility = 3e-4 ref-p= 1.0 refcoord_scaling = all pbc = xyz constraints = h-bonds Could anybody tell me what's wrong with my .mdp file? Thanks in advance. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] LINSC WARNING
Hi, Start by learning what makes a time step stable, e.g. manual 6.8 Mark On Fri, May 22, 2015 at 10:51 AM Vy Phan phanvy120...@gmail.com wrote: Dear Gromacs Users, When I run npt equilibrium, I set the step size is 4fs. I go many LINCS WARNING bonds that rotate more than 30 degrees When I reduce the step size to 2fs. All thing is fine. Could someone here explain to me? Finally, I want to use step size is 4fs. Any suggestions for me? Thank you Tuong Vy -- 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] build nuance in gmx5 (avoiding file INSTALL cannot find gmx)
Hi, On Thu, May 21, 2015 at 5:50 PM Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Szilárd: I report it only because it is allowed in gmx4 builds (or at least it works, I am not sure whether or not is it allowed). Along with the transition to the wrapper binary in 5.0, we changed where the binaries are placed in the build tree before they are installed, and this seems to interact badly in your case with how CMake install works (because both refer to the same bin subdirectory). We never intended people to try to do this, and I have seen someone else on this list have problems with it, so I have prepared a patch to stop people doing this. I move the source because I often have many modified source trees that I rename to keep things straight. The quick and dirty method that you cite presumes that one has root access, which is very unlikely on the places that most simulations are run. The http://www.gromacs.org/Documentation/Installation_Instructions_5.0#typical-gromacs-installation section below that does have a note about -DCMAKE_INSTALL_PREFIX=xxx to install GROMACS to a non-standard location (default /usr/local/gromacs) but that gives no suggestions on how to use it and based on my experience I presume that -DCMAKE_INSTALL_PREFIX=$(pwd) would give a similar error if applied to the quick and dirty method. There's several mentions of CMAKE_INSTALL_PREFIX further down in the install guide, and the point of the quick and dirty and typical build sections is to give people a way to know important things without a big pile of details. I have reorganized a bit at https://gerrit.gromacs.org/#/c/4647/ so there can be a link from the typical build to some discussion of what to do, and text to suggest people do not try Chris's approach. My intention is not to try to get gromacs to change the build procedure. Just to report something that worked once that no longer works and to include a snippit from the relevant error message so that it is searchable. Thanks, Mark Thank you, Chris. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Szilárd Páll pall.szil...@gmail.com Sent: 21 May 2015 11:24 To: Discussion list for GROMACS users Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] build nuance in gmx5 (avoiding file INSTALL cannot find gmx) You can't install into the build tree, AFAIK that's not allowed! Install into a clean target directory instead. Also, you mkdir source; mv * source step is just weird. Why move the source around? Instead you can simply create a build directory - this can even be in the source tree just as the uiqck and dirty install steps suggest: http://www.gromacs.org/Documentation/Installation_Instructions_5.0#quick-and-dirty-installation -- Szilárd On Thu, May 21, 2015 at 5:11 PM, Christopher Neale chris.ne...@alum.utoronto.ca wrote: Dear Users: This is just a note about compiling gromacs 5 so that the solution can be found by others if they need it. I used to compile gromacs like this: download and unpack tarball cd gromacs-5.0.5 mkdir source mv * source mkdir exec cd exec ** run my build script from here, using CMAKE_INSTALL_PREFIX=$(pwd) However, that no longer works. What happens is that make creates ./bin/gmx and then make install removes ./bin/gmx and then complains that it does not exist: CMake Error at src/programs/cmake_install.cmake:42 (file): file INSTALL cannot find /project2/p/pomes/cneale/GPC/exe/intel/gromacs-5.0.5/exec/bin/gmx. Call Stack (most recent call first): src/cmake_install.cmake:40 (include) cmake_install.cmake:48 (include) My solution was to build in a separate directory from either the source or the executable: download and unpack tarball cd gromacs-5.0.5 mkdir source mv * source mkdir exec build cd build ** run my build script from here, using CMAKE_INSTALL_PREFIX=$(pwd)/../exec Perhaps this is standard practice. Anyway, my original procedure works for gmx4.6.7 but not gmx5.0.5 so I thought I would report it. Note that this is separate from the issue that some have reported where a CMAKE_INSTALL_PREFIX using $(pwd) did not install but using the explicit path worked (I tested the explicit paths and got the same error that I report above). Chris. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read
Re: [gmx-users] How to connect different parts of a polymer?
Hi, Given .rtp entries for the repeat units, pdb2gmx can use the specbond.dat mechanism to generate cross-links, as it does e.g. for disulfide links in proteins. See manual. Mark On Fri, May 22, 2015 at 12:12 PM faride badalkhani farideh.kham...@gmail.com wrote: Dear GMX users I am trying to parametrize GROMOS FF for PAMAM dendrimers. I have paramerized core of the dendrimer, its repeat units, and terminal groups separately. but I dont know how to connect them to build a complete dendrimer so that GROMACS can recognize dendrimer structure exactly. Could you help me, please? Truly yours, Farideh -- 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] Pull code
Dear Justin, I want to simulate my triple helix using SMD, Can I use umbrella + distance? I saw many people doing SMD simulation by fixing one end and pull another end in their journal. Besides, my triple helix deviates a bit from Z axis, but I do not know the angle. I checked both dim for distance and pull-vec for direction, and found both of them needs pull direction. If I set dim = N N Y, will the force-deformation be reliable? Thanks. -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Thursday, 23 April 2015 10:33 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Pull code On 4/22/15 8:03 PM, Ming Tang wrote: Hi, Justin I am confusing about what is the difference between the rigid constraint in constraint pull method and the harmonic potential using umbrella. The force acts directly on the centre of mass of the group in constraint, and the force acts on the center of mass of the group through a spring when using umbrella pull method. Am I right? There is of course no difference in the fact that the two groups are restrained between their COM. The difference comes in how the force is applied and how the positions are updated. It's just like bonds. A harmonic bond (connection, restraint, whatever) oscillates about some mean value. That's the deal with the umbrella harmonic restraint. There is a target value, and the deviation from that target determines the magnitude of the force applied along the restraint vector to give rise to that target. With the constraint method, the positions are updated with SHAKE (as stated in the manual). A difference vector is calculated between the current position and the target position. The positions of the groups are then updated along that vector such that the rigid constraint is satisfied. It's the difference between being connected with a spring and being connected with a lead pipe. -Justin -Original Message- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin Lemkul Sent: Thursday, 23 April 2015 9:22 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Pull code On 4/22/15 7:17 PM, Ming Tang wrote: Hi，Alex You can try constraint. In umbrella， both 2 groups move. Not really. The constraint option keeps a rigid constraint between the two groups. The umbrella keyword specifies a harmonic potential, whose strength is tunable. Otherwise, the two methods are identical. If one group needs to stay in place, it needs position restraints applied to it. If the desired separation is not occurring, either a larger spring force constant or a faster pull rate is needed. -Justin Sent from my Huawei Mobile Alex nedoma...@gmail.com wrote: Hi all, I have a group (DNA) I'd like to translate relative to the other group (CNT) along the Z-direction so that DNA is the only group that's actually moving. The code I had prior to what I have now worked under GMX 4.5.something. Since the syntax has changed in 5.0.x, I found Justin's old suggestions, and this is what I have now: ;Pull code pull= umbrella pull_geometry = direction pull_coord1_vec = 0.0 0.0 1.0 pull_start = yes pull_coord1_init= 0.0 pull_ngroups= 2 pull_ncoords= 1 pull_coord1_groups = 1 2 pull_group1_name= CNT pull_group2_name= DNA pull_coord1_rate1 = 0.0002 ;nm per ps pull_coord1_k = 5000 ; kJ mol^-1 nm^-2 ;end pull code Does this look right? My simulation isn't nearly done, but I am looking at the Z-displacement in pullx.xvg and it just oscillates around a single value. The simulated time is now about 1.5 ns. Thank you, Alex -- 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 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit
Re: [gmx-users] How can i install DSSP for gromacs on centos6?
Hi, Searching google would have been faster for you ;-) There's a few hundred posts about how to get DSSP working with do_dssp. If you want to use such an old version of GROMACS, you'll need to use an old version of DSSP, because DSSP 2 changed how it accepts input and won't accept the old version at all. Mark On Fri, May 22, 2015 at 10:09 AM Homa rooz ha.roozbah...@gmail.com wrote: Hi there I tried to execute dssp for gromacs 4.5.7 by following this instruction: #sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 https://www.researchgate.net/go.Deref.html?url=ftp%3A%2F%2Fftp.cmbi.ru.nl%2Fpub%2Fsoftware%2Fdssp%2Fdssp-2.0.4-linux-amd64 -O /usr/local/bin/dssp #sudo chmod a+x /usr/local/bin/dssp #export DSSP=/usr/local/bin/dssp then I run g_do_dssp and I got this error: - Program g_do_dssp, VERSION 4.5.7 Source code file: /builddir/build/BUILD/gromacs-4.5.7/src/tools/do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddKnNFex ddYd8PhB /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors https://www.researchgate.net/go.Deref.html?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FErrors --- It also makes some files like ddYd8PhB! I have tried two different binary file but it didn't work. In addition there is a binary g_do_dssp from gromacs package . How can I point it to export dssp? plz help me to fix that problem -- Homa Ahmadi Shahed University Faculty of Basic Sciences Alternative email h.ahm...@shahed.ac.ir h.ahm...@ast.ui.ac.ir -- 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] distance constrain of two groups
Dear all, After energy minimization, I want to equilibrate my triple helix using NPT, but need to keep its general shape, as I want to study the load-deformation relationship including the triple helix unfolding stage. During the equilibration, I want to fix the distance between the centre of mass of two group atoms along the vector connecting the two groups. Could anybody tell me how can I do this？ Thanks in advance. -- 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] Generate the water box
Use gmx editconf first to create the box then gmx solvate to fill it with water (omitting -box directive this time). -- James Wes Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu LinkedIn From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Vy Phan phanvy120...@gmail.com Sent: Thursday, May 21, 2015 8:36 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Generate the water box Dear all, I can generate the cubic box or the rectangular box with gmx solvate -cs water.gro -box but I would like to have the octahedron box.I try many way but I can not. How I can do it? Thank a lot Tuong Vy 2015-05-21 1:49 GMT+09:00 Justin Lemkul jalem...@vt.edu: On 5/20/15 11:55 AM, 姚懿 wrote: genbox without adding a protein. More specifically (and for 5.0): gmx solvate -cs water.gro -box (whatever size is needed) -Justin On Wed, May 20, 2015 at 9:56 AM, Vy Phan phanvy120...@gmail.com wrote: Dear Gromacs Users, Can I generate only water on the Gromacs? I need water box only. Thank you Tuong Vy -- 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 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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] do_dssp
Yes On Fri, May 22, 2015 at 2:59 PM MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Hi Gromacs users, I did my simulations using an older version of GROMACS (ie 4.5.7) and after reading through various posts, it seems I have to do the dssp analysis using a newer version. Can I use the trajectories I got from the previous older version of GROMACS to perform dssp analysis on Gromacs 5.0.5? Thanks Tom -- 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] LINSC WARNING
Thank a lot for your suggestion. Tuong VY 2015-05-22 20:21 GMT+09:00 Mark Abraham mark.j.abra...@gmail.com: Hi, Start by learning what makes a time step stable, e.g. manual 6.8 Mark On Fri, May 22, 2015 at 10:51 AM Vy Phan phanvy120...@gmail.com wrote: Dear Gromacs Users, When I run npt equilibrium, I set the step size is 4fs. I go many LINCS WARNING bonds that rotate more than 30 degrees When I reduce the step size to 2fs. All thing is fine. Could someone here explain to me? Finally, I want to use step size is 4fs. Any suggestions for me? Thank you Tuong Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] 4 Titan X or 2?
On 22 May 2015, at 15:51, Albert mailmd2...@gmail.com wrote: Hello: I am going to perform MD simulation for a typical biological system with 60,000-80,000 atoms in all. Amber FF would be used for the whole system. I am just wondering will a 4x Titan X much faster than 2xTitan X? That depends on what hardware you want to pair these with on the CPU side. Carsten thanks a lot Albert -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] H-bond query
Hello all, I am trying to see what happens to the no. of Watson-Crick hydrogen bonds between two parallel chains of a double stranded DNA on incorporating a flat graphene sheet. The no of interchain H-bonds are supposed to decrease with time. But I am not sure how to use g_hbond in order to demonstrate this. How should I make index groups for the two chains of DNA? Should I take all the atoms into account (except backbone) and then index them like chain_A and chain_B and then analyze the hbnum.xvg file from g_hbond? Furthermore, in the hbnum.xvg file the third column represents the no. of H-bond within the distance cut-off and the 2nd one is the total no of hydrogen bonds as a function of simulation time. So, which one should I plot in this case against time? Your help is required. Soumadwip Research Fellow IITB 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.
[gmx-users] do_dssp
Hi Gromacs users, I did my simulations using an older version of GROMACS (ie 4.5.7) and after reading through various posts, it seems I have to do the dssp analysis using a newer version. Can I use the trajectories I got from the previous older version of GROMACS to perform dssp analysis on Gromacs 5.0.5? Thanks Tom -- 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] LINSC WARNING
Hi Phan, If you want to use the time step of 4 fs, you can try to use virtual sites (gmx pdb2gmx -f ... -vsite hydrogens). Please look at the following web site. https://www.wenmr.eu/wenmr/md-simulations-using-gromacs-web-server Virtual sites:The use of virtual sites offers another possibility to increase the efficiency of the simulation. These are used to replace hydrogen atoms, removing the fastest vibrations in the system that otherwise limit the time step that can be used. Simulations run with virtual sites can therefore use a time step of 4 fs, instead of the 2 fs that is used for simulations with explicit hydrogen atoms 2015-05-22 15:27 GMT+02:00 Vy Phan phanvy120...@gmail.com: Thank a lot for your suggestion. Tuong VY 2015-05-22 20:21 GMT+09:00 Mark Abraham mark.j.abra...@gmail.com: Hi, Start by learning what makes a time step stable, e.g. manual 6.8 Mark On Fri, May 22, 2015 at 10:51 AM Vy Phan phanvy120...@gmail.com wrote: Dear Gromacs Users, When I run npt equilibrium, I set the step size is 4fs. I go many LINCS WARNING bonds that rotate more than 30 degrees When I reduce the step size to 2fs. All thing is fine. Could someone here explain to me? Finally, I want to use step size is 4fs. Any suggestions for me? Thank you Tuong Vy -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Ahmet Yıldırım -- 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] 4 Titan X or 2?
Hello: I am going to perform MD simulation for a typical biological system with 60,000-80,000 atoms in all. Amber FF would be used for the whole system. I am just wondering will a 4x Titan X much faster than 2xTitan X? thanks a lot Albert -- 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] 4 Titan X or 2?
how about the following: 2 x Intel Xeon E52680V3,12 cores, 2.53.3 GHz Cool Silent Features Supermicro dual Xeon motherboard 64GB ECC DDR4 RAM 4channel 2133 MHz, 8 x 8 GB 256GB Samsung SSD 850 PRO 2 x 6000 GB WD Red hard drive, 7200 rpm Asus GTX TITAN X, 12 GB GDDR5 Asus GTX TITAN X, 12 GB GDDR5 Asus GTX TITAN X, 12 GB GDDR5 Asus GTX TITAN X, 12 GB GDDR5 Supermicro Server tower / rack housing, 4 x GPU, 8 x hotswap bays 2000W redundant power supply On 05/22/2015 04:04 PM, Kutzner, Carsten wrote: That depends on what hardware you want to pair these with on the CPU side. Carsten -- 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] LINSC WARNING
Hi, On Fri, May 22, 2015 at 3:57 PM Albert mailmd2...@gmail.com wrote: that's interesting. How about the ligand in the system? The hydrogen should also be treated in virtual site? Is it possible treat the binding pocket as explicit atoms, and all the rest in virtual hydrogen? You're probably thinking of united atoms, which are entirely distinct. You can read all about virtual sites in the manual and publications ;-) Does it support GPU? Yes Mark thx a lot Albert On 05/22/2015 03:51 PM, Ahmet Yıldırım wrote: Hi Phan, If you want to use the time step of 4 fs, you can try to use virtual sites (gmx pdb2gmx -f ... -vsite hydrogens). Please look at the following web site. https://www.wenmr.eu/wenmr/md-simulations-using-gromacs-web-server Virtual sites:The use of virtual sites offers another possibility to increase the efficiency of the simulation. These are used to replace hydrogen atoms, removing the fastest vibrations in the system that otherwise limit the time step that can be used. Simulations run with virtual sites can therefore use a time step of 4 fs, instead of the 2 fs that is used for simulations with explicit hydrogen atoms -- 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] do_dssp
Thanks Mark. On Fri, May 22, 2015 at 3:17 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Yes On Fri, May 22, 2015 at 2:59 PM MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Hi Gromacs users, I did my simulations using an older version of GROMACS (ie 4.5.7) and after reading through various posts, it seems I have to do the dssp analysis using a newer version. Can I use the trajectories I got from the previous older version of GROMACS to perform dssp analysis on Gromacs 5.0.5? Thanks Tom -- 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. *To all the people you can,As long as ever you can. - John Wesley. * -- 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] LINSC WARNING
that's interesting. How about the ligand in the system? The hydrogen should also be treated in virtual site? Is it possible treat the binding pocket as explicit atoms, and all the rest in virtual hydrogen? Does it support GPU? thx a lot Albert On 05/22/2015 03:51 PM, Ahmet Yıldırım wrote: Hi Phan, If you want to use the time step of 4 fs, you can try to use virtual sites (gmx pdb2gmx -f ... -vsite hydrogens). Please look at the following web site. https://www.wenmr.eu/wenmr/md-simulations-using-gromacs-web-server Virtual sites:The use of virtual sites offers another possibility to increase the efficiency of the simulation. These are used to replace hydrogen atoms, removing the fastest vibrations in the system that otherwise limit the time step that can be used. Simulations run with virtual sites can therefore use a time step of 4 fs, instead of the 2 fs that is used for simulations with explicit hydrogen atoms -- 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] LINSC WARNING
I haven't tried vsites on GPU. I just used them for the united atom ffs (espically GROMOS ffs) with reaction field method. Actually I didn't get good results about the ligand in the system. Maybe the problem was force field (54A7) I used. Because for GROMOS ffs there is another problem that is helix melting :). 2015-05-22 16:08 GMT+02:00 Mark Abraham mark.j.abra...@gmail.com: Hi, On Fri, May 22, 2015 at 3:57 PM Albert mailmd2...@gmail.com wrote: that's interesting. How about the ligand in the system? The hydrogen should also be treated in virtual site? Is it possible treat the binding pocket as explicit atoms, and all the rest in virtual hydrogen? You're probably thinking of united atoms, which are entirely distinct. You can read all about virtual sites in the manual and publications ;-) Does it support GPU? Yes Mark thx a lot Albert On 05/22/2015 03:51 PM, Ahmet Yıldırım wrote: Hi Phan, If you want to use the time step of 4 fs, you can try to use virtual sites (gmx pdb2gmx -f ... -vsite hydrogens). Please look at the following web site. https://www.wenmr.eu/wenmr/md-simulations-using-gromacs-web-server Virtual sites:The use of virtual sites offers another possibility to increase the efficiency of the simulation. These are used to replace hydrogen atoms, removing the fastest vibrations in the system that otherwise limit the time step that can be used. Simulations run with virtual sites can therefore use a time step of 4 fs, instead of the 2 fs that is used for simulations with explicit hydrogen atoms -- 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. -- Ahmet Yıldırım -- 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] 4 Titan X or 2?
On 22 May 2015, at 16:08, Albert mailmd2...@gmail.com wrote: how about the following: 2 x Intel Xeon E52680V3,12 cores, 2.53.3 GHz My guess is that two TITAN X will be more than enough to balance the CPU compute power. To save some money, you could also start with two GTX 980 instead of the TITANs and upgrade to four GTX 980 if you need more power on the GPU side. Carsten Cool Silent Features Supermicro dual Xeon motherboard 64GB ECC DDR4 RAM 4channel 2133 MHz, 8 x 8 GB 256GB Samsung SSD 850 PRO 2 x 6000 GB WD Red hard drive, 7200 rpm Asus GTX TITAN X, 12 GB GDDR5 Asus GTX TITAN X, 12 GB GDDR5 Asus GTX TITAN X, 12 GB GDDR5 Asus GTX TITAN X, 12 GB GDDR5 Supermicro Server tower / rack housing, 4 x GPU, 8 x hotswap bays 2000W redundant power supply On 05/22/2015 04:04 PM, Kutzner, Carsten wrote: That depends on what hardware you want to pair these with on the CPU side. Carsten -- 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. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/grubmueller/kutzner http://www.mpibpc.mpg.de/grubmueller/sppexa -- 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] Editconf error
Here are the coordinates from my pdb file: ATOM 1 N MET G 27 69.331 43.147 76.443 1.00 0.00 N ATOM 2 CA MET G 27 68.996 44.047 75.331 1.00 0.00 C ATOM 3 C MET G 27 67.818 43.550 74.510 1.00 0.00 C ATOM 4 O MET G 27 66.981 44.264 73.969 1.00 0.00 O ATOM 5 CB MET G 27 70.152 44.201 74.325 1.00 0.00 C ATOM 6 CG MET G 27 70.024 45.547 73.614 1.00 0.00 C ATOM 7 SD MET G 27 70.710 46.841 74.678 1.00 0.00 S ATOM 8 CE MET G 27 70.252 48.118 73.481 1.00 0.00 C ATOM 9 N ALA G 28 67.504 42.250 74.523 1.00 0.00 N ATOM 10 CA ALA G 28 66.247 41.666 74.095 1.00 0.00 C ATOM 11 C ALA G 28 64.968 42.391 74.469 1.00 0.00 C ATOM 12 O ALA G 28 64.064 42.543 73.651 1.00 0.00 O ATOM 13 CB ALA G 28 66.323 40.167 74.396 1.00 0.00 C ATOM 14 N GLU G 29 64.839 42.732 75.756 1.00 0.00 N ATOM 15 CA GLU G 29 63.656 43.315 76.334 1.00 0.00 C ATOM 16 C GLU G 29 63.567 44.789 75.955 1.00 0.00 C ATOM 17 O GLU G 29 62.480 45.354 75.850 1.00 0.00 O ATOM 18 CB GLU G 29 63.662 43.143 77.854 1.00 0.00 C ATOM 19 CG GLU G 29 64.822 43.835 78.553 1.00 0.00 C ATOM 20 CD GLU G 29 64.794 43.644 80.055 1.00 0.00 C ATOM 21 OE1 GLU G 29 63.801 44.058 80.689 1.00 0.00 O ATOM 22 OE2 GLU G 29 65.765 43.078 80.601 1.00 0.00 O1- And here are the coordinates from the .gro file Giant Rising Ordinary Mutants for A Clerical Setup 16231 27MET N1 6.933 4.315 7.644 27MET H12 7.011 4.352 7.695 27MET H23 6.854 4.307 7.705 27MET H34 6.957 4.224 7.608 27MET CA5 6.900 4.405 7.533 27MET HA6 6.878 4.489 7.582 27MET CB7 7.015 4.420 7.432 27METHB18 7.103 4.416 7.481 27METHB29 7.011 4.346 7.365 27MET CG 10 7.002 4.555 7.361 27METHG1 11 7.052 4.545 7.275 27METHG2 12 6.905 4.567 7.343 27MET SD 13 7.071 4.684 7.468 27MET CE 14 7.025 4.812 7.348 27METHE1 15 7.053 4.901 7.383 27METHE2 16 7.071 4.794 7.261 27METHE3 17 6.926 4.811 7.334 27MET C 18 6.782 4.355 7.451 27MET O 19 6.698 4.426 7.397 28ALA N 20 6.750 4.225 7.452 28ALA H 21 6.820 4.162 7.486 28ALA CA 22 6.625 4.167 7.410 28ALA HA 23 6.620 4.184 7.311 28ALA CB 24 6.632 4.017 7.440 28ALAHB1 25 6.547 3.973 7.411 28ALAHB2 26 6.709 3.976 7.389 28ALAHB3 27 6.646 4.003 7.538 28ALA C 28 6.497 4.239 7.447 28ALA O 29 6.406 4.254 7.365 29GLU N 30 6.484 4.273 7.576 29GLU H 31 6.562 4.257 7.636 29GLU CA 32 6.366 4.332 7.633 29GLU HA 33 6.289 4.281 7.594 29GLU CB 34 6.366 4.314 7.785 29GLUHB1 35 6.281 4.352 7.822 29GLUHB2 36 6.371 4.217 7.806 29GLU CG 37 6.482 4.384 7.855 29GLUHG1 38 6.568 4.346 7.820 29GLUHG2 39 6.478 4.481 7.836 29GLU CD 40 6.479 4.364 8.005 29GLUOE1 41 6.380 4.406 8.069 29GLUOE2 42 6.576 4.308 8.060 29GLU C 43 6.357 4.479 7.595 29GLU O 44 6.248 4.535 7.585 and this is the output from editconf. Giant Rising Ordinary Mutants for A Clerical Setup 16231 27MET N1-nan-nan-nan 27MET H12-nan-nan-nan 27MET H23-nan-nan-nan 27MET H34-nan-nan-nan 27MET CA5-nan-nan-nan 27MET HA6-nan-nan-nan 27MET CB7-nan-nan-nan 27METHB18-nan-nan-nan 27METHB29-nan-nan-nan 27MET CG 10-nan-nan-nan 27METHG1 11-nan-nan-nan 27METHG2 12-nan-nan-nan 27MET SD 13-nan-nan-nan 27MET CE 14-nan-nan-nan 27METHE1 15-nan-nan-nan 27METHE2 16-nan-nan-nan 27METHE3 17-nan-nan-nan 27MET C 18-nan-nan-nan 27MET O 19-nan-nan-nan I hope that this helps. Thanks 2015-05-20 22:28 GMT-03:00 Justin Lemkul jalem...@vt.edu: On 5/20/15 5:27 PM, Jorge Dagnino wrote: Dear GMX users. Im trying to create my system and When i use pdb2gmx everything seems ok. gmx pdb2gmx -f trim.pdb -o trim.gro -water spce -chainsep id Including chain 1 in system: 3235 atoms 203 residues
[gmx-users] conserved energy
Dear users, The total energy obtained from the .edr file is the sum of potential and kinetic energy of system. But there is not any information about conserved energy in manual. Maybe I couldn't find it. I am looking for answers of the following questions: -Which energy contributions/terms does the conserved energy include? -How I get individual contributions (like constrains' contribution) to the conserved energy? Any help will be appreciated. -- Ahmet Yıldırım -- 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] Editconf error
It'd be more helpful for troubleshooting your problem if you post the entire file in each case, not just parts of them. If it's a large file use Pastebin.com or something similar. -- James Wes Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu LinkedIn From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Jorge Dagnino jdagn...@gmail.com Sent: Friday, May 22, 2015 11:06 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Editconf error Here are the coordinates from my pdb file: ATOM 1 N MET G 27 69.331 43.147 76.443 1.00 0.00 N ATOM 2 CA MET G 27 68.996 44.047 75.331 1.00 0.00 C ATOM 3 C MET G 27 67.818 43.550 74.510 1.00 0.00 C ATOM 4 O MET G 27 66.981 44.264 73.969 1.00 0.00 O ATOM 5 CB MET G 27 70.152 44.201 74.325 1.00 0.00 C ATOM 6 CG MET G 27 70.024 45.547 73.614 1.00 0.00 C ATOM 7 SD MET G 27 70.710 46.841 74.678 1.00 0.00 S ATOM 8 CE MET G 27 70.252 48.118 73.481 1.00 0.00 C ATOM 9 N ALA G 28 67.504 42.250 74.523 1.00 0.00 N ATOM 10 CA ALA G 28 66.247 41.666 74.095 1.00 0.00 C ATOM 11 C ALA G 28 64.968 42.391 74.469 1.00 0.00 C ATOM 12 O ALA G 28 64.064 42.543 73.651 1.00 0.00 O ATOM 13 CB ALA G 28 66.323 40.167 74.396 1.00 0.00 C ATOM 14 N GLU G 29 64.839 42.732 75.756 1.00 0.00 N ATOM 15 CA GLU G 29 63.656 43.315 76.334 1.00 0.00 C ATOM 16 C GLU G 29 63.567 44.789 75.955 1.00 0.00 C ATOM 17 O GLU G 29 62.480 45.354 75.850 1.00 0.00 O ATOM 18 CB GLU G 29 63.662 43.143 77.854 1.00 0.00 C ATOM 19 CG GLU G 29 64.822 43.835 78.553 1.00 0.00 C ATOM 20 CD GLU G 29 64.794 43.644 80.055 1.00 0.00 C ATOM 21 OE1 GLU G 29 63.801 44.058 80.689 1.00 0.00 O ATOM 22 OE2 GLU G 29 65.765 43.078 80.601 1.00 0.00 O1- And here are the coordinates from the .gro file Giant Rising Ordinary Mutants for A Clerical Setup 16231 27MET N1 6.933 4.315 7.644 27MET H12 7.011 4.352 7.695 27MET H23 6.854 4.307 7.705 27MET H34 6.957 4.224 7.608 27MET CA5 6.900 4.405 7.533 27MET HA6 6.878 4.489 7.582 27MET CB7 7.015 4.420 7.432 27METHB18 7.103 4.416 7.481 27METHB29 7.011 4.346 7.365 27MET CG 10 7.002 4.555 7.361 27METHG1 11 7.052 4.545 7.275 27METHG2 12 6.905 4.567 7.343 27MET SD 13 7.071 4.684 7.468 27MET CE 14 7.025 4.812 7.348 27METHE1 15 7.053 4.901 7.383 27METHE2 16 7.071 4.794 7.261 27METHE3 17 6.926 4.811 7.334 27MET C 18 6.782 4.355 7.451 27MET O 19 6.698 4.426 7.397 28ALA N 20 6.750 4.225 7.452 28ALA H 21 6.820 4.162 7.486 28ALA CA 22 6.625 4.167 7.410 28ALA HA 23 6.620 4.184 7.311 28ALA CB 24 6.632 4.017 7.440 28ALAHB1 25 6.547 3.973 7.411 28ALAHB2 26 6.709 3.976 7.389 28ALAHB3 27 6.646 4.003 7.538 28ALA C 28 6.497 4.239 7.447 28ALA O 29 6.406 4.254 7.365 29GLU N 30 6.484 4.273 7.576 29GLU H 31 6.562 4.257 7.636 29GLU CA 32 6.366 4.332 7.633 29GLU HA 33 6.289 4.281 7.594 29GLU CB 34 6.366 4.314 7.785 29GLUHB1 35 6.281 4.352 7.822 29GLUHB2 36 6.371 4.217 7.806 29GLU CG 37 6.482 4.384 7.855 29GLUHG1 38 6.568 4.346 7.820 29GLUHG2 39 6.478 4.481 7.836 29GLU CD 40 6.479 4.364 8.005 29GLUOE1 41 6.380 4.406 8.069 29GLUOE2 42 6.576 4.308 8.060 29GLU C 43 6.357 4.479 7.595 29GLU O 44 6.248 4.535 7.585 and this is the output from editconf. Giant Rising Ordinary Mutants for A Clerical Setup 16231 27MET N1-nan-nan-nan 27MET H12-nan-nan-nan 27MET H23-nan-nan-nan 27MET H34-nan-nan-nan 27MET CA5-nan-nan-nan 27MET HA6-nan-nan-nan 27MET CB7-nan-nan-nan 27METHB18-nan-nan-nan 27METHB29-nan-nan-nan 27MET CG 10-nan-nan-nan 27METHG1 11-nan-nan-nan 27METHG2
