Re: [gmx-users] OPLSAA parameters
Elisabeth wrote: Hello to all, I am looking for bonded and nonbonded parameters for C H atoms in saturated hydrocarbons. atom types are: Carbon atoms opls_135 opls_136 H opls_140 opls_135 12.01100 ; alkane CH3 opls_136 12.01100 ; alkane CH2 opls_1401.00800 ; alkane H. Please help me out with the following: - I am wondering if I am selecting the correct values, for C-C and C-H bonds from ffoplsaabon.itp. The C-C bond is not correct for alkanes. It is for the C-C bond of oxalic acid, as the comment indicates. In ffnonbonded.itp, you can see how opls_* types are mapped to different bonded atom types (for instance, opls_135/136 are CT). Note that in the topology, you do not have to explicitly define values when using OPLS-AA; any bond between two defined bonded atom types will be automatically detected and used. C C 10.15100 292880.0 ; wlj oxalic acid, etc. HCC 10.10900 284512.0 ; wlj 7/96 - what does wlj mean? Probably someone's initials, which occur frequently to indicate either the source of the parameters or the individual that added them. In this case, my guess would be Jorgensen is the referenced individual here. - what are the units? This is in the manual. Angle CA CA CZ 1 120.000585.760 ; wlj CA CA CR 1 120.000527.184 ; CA CA CX 1 120.000711.280 ; C CT Cl 1 109.800577.392 ; wlj - I can not distinguish CA CZ What are they referring to? See the above tip about converting atom types in ffnonbonded.itp. [ dihedraltypes ] C C CT HC 3 0.17782 0.53346 0.0 -0.71128 0.0 0.0 ; dicarbonyls BMC 8,1881(2000) - Is this what I need for oplsaa 135 136 140? Probably not. The comment indicates the dihedral is for dicarbonyls. The appropriate dihedral is: CT CT CT HC 3 0.62760 1.88280 0.0 -2.51040 0.0 0.0 ; hydrocarbon all-atom Note how the comment indicates it is for use with hydrocarbons. Again, like bonds as described above, you do not need to explicitly list parameters in the topology. They will be inferred from the atom types. ffoplsaanb.itp. opls_135 CT6 12.01100-0.180 A3.5e-01 2.76144e-01 opls_136 CT6 12.01100-0.120 A3.5e-01 2.76144e-01 opls_140 HC1 1.00800 0.060 A2.5e-01 1.25520e-01 - are these parameters for opls_135 12.01100 ; alkane CH3 opls_136 12.01100 ; alkane CH2 opls_1401.00800 ; alkane H. ? Yes. Also in usr/local/gromacs/share/gromacs/top/ directory I can not find ffoplsaanb,itp and ffoplsaabon.itp for 4.5.4 whereas in previous versions these files were accessible. I am using itp files from version 4.0.7 and wanted to make sure the above parameters for oplsa_135 oplsa_136 and oplsa_140 have been remained unchanged in 4.5.4. Where can I find these files? The force field organization has changed, but the content of the force fields has not. This is described in the manual. All the equivalent files are now in the oplsaa.ff subdirectory. For backwards compatibility, the statement #include "ffoplsaa.itp" will indeed call the force field, because you will note that ffoplsaa.itp now simply calls the correct force field with #include "oplsaa.ff/forcefield.itp." -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] distance and angle cutoff for hydrogen bond
Dear gromacs users in gromacs manual, there is [-a real 30 Cutoff angle (degrees, Acceptor - Donor - Hydrogen) -r real 0.35 Cutoff radius (nm, X - Acceptor, see next option)] I think that in hb (D-H...A) distance of 0.35 nm = distance between D and A. and angle of 30 = acceptor-donor–hydrogen angle. is my think true? if I want following criterion for hydrogen bond analysis, is [ -r 3.5 and -a 135 ] true? donor-acceptor distance (dDA) ≤ 3.5 Å and the donor–hydrogen-acceptor angle (αDHA) ≥ 135°. any help will highly appreciated. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] calculate potential in the box contain ions
Deer users The simulation box contains sodium and chloride ions start simulation pdb2gmx -f ion.pdb -posrefc 0 Force Field : AMBER99SB-ILDN - Water TIP3P editconf -f conf.gro -bt cubic -box 3 3 3 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f minim.mdp -c 5.gro -p topol.top mdrun -s topol.tpr grompp -f nvt.mdp -c confout.gro -p topol.top -o md.tpr mdrun -s md.tpr Whether the simulation iscorrect ? ion.pdb Description: Binary data minim.mdp Description: Binary data nvt.mdp Description: Binary data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] calculate potential in the box contain ions
Dear users The simulation box contains sodium and chloride ions start simulation pdb2gmx -f ion.pdb -posrefc 0 Force Field : AMBER99SB-ILDN - Water TIP3P editconf -f conf.gro -bt cubic -box 3 3 3 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f minim.mdp -c 5.gro -p topol.top mdrun -s topol.tpr grompp -f nvt.mdp -c confout.gro -p topol.top -o md.tpr mdrun -s md.tpr Whether the simulation and results iscorrect ? ion.pdb Description: Binary data minim.mdp Description: Binary data nvt.mdp Description: Binary data <><>-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] distance and angle cutoff for hydrogen bond
atila petrosian wrote: Dear gromacs users in gromacs manual, there is [-a real 30 Cutoff angle (degrees, Acceptor - Donor - Hydrogen) -r real 0.35 Cutoff radius (nm, X - Acceptor, see next option)] I think that in hb (D-H...A) distance of 0.35 nm = distance between D and A. and angle of 30 = acceptor-donor–hydrogen angle. is my think true? That's what the manual says. if I want following criterion for hydrogen bond analysis, is [ -r 3.5 and -a 135 ] true? No. Gromacs uses nm for distances. With -r 3.5, you calculate H-bonds that are 3.5 nm away. An angle of 135 for A-D-H means the H atom is pointed away from the acceptor, indicating that there really isn't a hydrogen bond. -Justin donor-acceptor distance (d_DA ) ≤ 3.5 Å and the donor–hydrogen-acceptor angle (α_DHA ) ≥ 135°. any help will highly appreciated. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] calculate potential in the box contain ions
Saeid Akbarshahi wrote: Deer users The simulation box contains sodium and chloride ions start simulation pdb2gmx -f ion.pdb -posrefc 0 Force Field : AMBER99SB-ILDN - Water TIP3P editconf -f conf.gro -bt cubic -box 3 3 3 genbox -cp out.gro -cs spc216.gro -o 5.gro -p topol.top grompp -f minim.mdp -c 5.gro -p topol.top mdrun -s topol.tpr grompp -f nvt.mdp -c confout.gro -p topol.top -o md.tpr mdrun -s md.tpr Whether the simulation is correct ? Is there some reason you think it isn't? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] umbrella sampling
Thanks very much. I am sorry I did not describe my question very clear. In my system, I am going to obtain three things. (1) the free energy versus distance, which I can obtain from g_wham. (2) the free energy versus, eg, the radius of gyration of the object A. (3) the 2-D free energy as a function of the radius of gyration of A and the radius of gyration of B. I do not know how to get (2) and (3). Your first method can help me obtain (2), but I can not obtain (3) because then it needs a 3-D WHAM code, am I correct? For your second method, I do not quite understand how to re-weighting using the F-values from 1D-WHAM. Could you please explain it? Thanks. Sincerely, Qian - Original Message - From: chris.ne...@utoronto.ca Date: Friday, July 29, 2011 11:00 pm Subject: [gmx-users] umbrella sampling To: gmx-users@gromacs.org > format your data for 2D-WHAM with 1D being the distance and the > 2nd-D being your other coordinate of interest. Specify a value > of zero for the force constants for your 2nd-D. Run 2D-WHAM. > Boltzmann project the 2D PMF onto your 2nd-D. > > I think you can also do essentially the same thing by re- > weighting using the F-values from 1D-WHAM, but I find the above > method to be the simplest. It also provides you with a 2D free > energy profile, which can be informative both biologically and > to indicate on sampling problems. > > Note that you're very likely going to run into convergence > problems since your 2nd-D will rely on brute-force to converge, > and worse: the umbrellas in 1D can force the sampling in the 2nd- > D to surmount energy barriers that might be circumvented in > unrestrained sampling. > > Chris. > > -- original message -- > > Qian Wang wrote: > Hi, > > I used umbrella sampling method to restrain the distance of two > molecules at several distances. Then I can use g_wham to get the free > energy as a function of the distance. Is there any way that I > can get > the free energy as a function of another parameter? Thanks a lot. > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] query on Free energy perturbation
Hi, I was planning to use Thermodynamic integration to calculate solvation free energy of a molecule in a solvent. I was following Justin Lemkul's online tutorial. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html . I found that a) a sd integrator is used in stead of usual md integrator ( Leap-Frog integrator). I was wondering whether is it a specific recommendation for thermodynamic integration to use stochastic integrator ? b) I also found DispCorr = EnerPres was also used to Apply long range dispersion corrections for Energy and Pressure . Is it also a recommendation to use with thermodyanmic integration technique ? Thanks Jagannath-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] query on Free energy perturbation
Sanku M wrote: Hi, I was planning to use Thermodynamic integration to calculate solvation free energy of a molecule in a solvent. I was following Justin Lemkul's online tutorial. http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html . I found that a) a sd integrator is used in stead of usual md integrator ( Leap-Frog integrator). I was wondering whether is it a specific recommendation for thermodynamic integration to use stochastic integrator ? It's simply a more accurate integrator for sensitive quantities for which solvent viscosity may be important. It also controls temperature via the Langevin method, which produces a proper canonical ensemble. b) I also found DispCorr = EnerPres was also used to Apply long range dispersion corrections for Energy and Pressure . Is it also a recommendation to use with thermodyanmic integration technique ? Dispersion correction is necessary when plain cutoffs are employed for quantities that are sensitive to such truncation artifacts. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] protein in membrane
Hi, I used the inflategro.pl script to insert my protein into the membrane and scaled down the lipids until it reached the recommended area per lipid value. After removing 4 lipid molecules, I started with an area of 90 square angstrom and reached a value of 65 square angstrom within just 5 iterations. However, when I had a look at my gro file, all my lipids look spaced out and there seems to be too much of gap between the lipids and the protein such that if I solvate it, I am pretty sure water molecules can easily occupy those cavities. I am wondering what would have possibly gone wrong?! Cheers Sweta __ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. __ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] protein in membrane
Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Thursday, August 4, 2011. For all questions about CloudBroker and the CloudBroker Platform, please contact the company under i...@cloudbroker.com or Nicola Fantini under nicola.fant...@cloudbroker.com. If you need to talk to me in person for urgent or important issues, please call my mobile phone number. Kind regards, Wibke Sudholt -- Dr. Wibke Sudholt CEO CloudBroker GmbH Technoparkstrasse 1 CH-8005 Zurich Switzerland Phone: +41 44 633 79 34 Email: i...@cloudbroker.com Web:http://www.cloudbroker.com -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] protein in membrane
Sweta Iyer wrote: Hi, I used the inflategro.pl script to insert my protein into the membrane and scaled down the lipids until it reached the recommended area per lipid value. After removing 4 lipid molecules, I started with an area of 90 square angstrom and reached a value of 65 square angstrom within just 5 iterations. However, when I had a look at my gro file, all my lipids look spaced out and there seems to be too much of gap between the lipids and the protein such that if I solvate it, I am pretty sure water molecules can easily occupy those cavities. I am wondering what would have possibly gone wrong?! Probably in unit conversion, but without knowing the initial inflation factor, it's hard to say for sure, but if you only reached 90 A^2 in the initial inflation I'd suspect you'd have a ton more lipids removed, even for a very small protein. Did you multiply the InflateGRO output by 10 or 100? The latter is correct to convert between nm^2 and A^2 (1 nm^2 = 100 A^2). You can always check progress using box vectors; if they are not close to the original membrane structure, you're not done. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] calculate potential in the box contain ions
Please keep the discussion on the list; I'm not a private tutor. Saeid Akbarshahi wrote: Dear Justin I have simulated this system with this structure and files.Could you tell me, is my structure correct? I have no clue what is in your system, what settings were used for the simulation, or anything else so I cannot make any assessment whatsoever. I am a novice user. It is in your best interest to do lots of homework before running a simulation and hoping it's right. Ask yourself: what protocols have others used? What have they analyzed? Why have they done these things? Unless you can answer all of these questions and understand the logic behind the choices made, you're not ready to do simulations if you rely on keeping your fingers crossed, hoping to have someone check your work for you. There is a steep learning curve for doing MD simulations properly, but doing the proper preparation now will save you tons of time (and wasted data) later on. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
