Dear Dr. Justin, Thanks for the clarification and sorry for the delayed response from my side. I am calculating flat bottom potential along with osmotic pressure values to verify my calculations. The flat bottom potential values calculated by in-house code matches with g_energy values. Thanks again.
On Dec 28, 2017 4:39 AM, <gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: Send gromacs.org_gmx-users mailing list submissions to gromacs.org_gmx-users@maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or, via email, send a message with subject or body 'help' to gromacs.org_gmx-users-requ...@maillist.sys.kth.se You can reach the person managing the list at gromacs.org_gmx-users-ow...@maillist.sys.kth.se When replying, please edit your Subject line so it is more specific than "Re: Contents of gromacs.org_gmx-users digest..." Today's Topics: 1. dielectric constant effect on protein, dna, water interface (Sarath Chandra) 2. More dihedrals generated than provided in the force field & "No default Proper Dih. types" as a result (Timofey Tyugashev) 3. Re: More dihedrals generated than provided in the force field & "No default Proper Dih. types" as a result (Justin Lemkul) 4. Re: regarding calculation of intra-residue energy (Justin Lemkul) 5. Re: Osmotic Pressure Calculations and fixed reference values of walls (Justin Lemkul) 6. Strange energy values with GMX 5.1, PME and Verlet (Diana Lousa) ---------------------------------------------------------------------- Message: 1 Date: Wed, 27 Dec 2017 18:00:36 +0530 From: Sarath Chandra <sarathchandrada...@gmail.com> To: Discussion list for GROMACS users <gmx-us...@gromacs.org> Subject: [gmx-users] dielectric constant effect on protein, dna, water interface Message-ID: <CAKi3H2XEvG0UxJpomMZM1xz4RydTguBhRBs=o-ddnmqvq_3...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Fellow users, I am working on a Protein-DNA complex and I have a question regarding the electrostatic interaction energies calculated at the interface of protein, DNA and water. I am using amber99sb+parambsc0 forcefield for my system with TIP3P water simulated using gromacs4.6.4. I understand that the additive forcefield does not capture polarizibility well. I have already referred to articles on PME but it is not clear if the PME takes into account the dielectric constant change at the protein, DNA, water interface. During the electrostatic forces calculation is this captured by calculation of local dipole moments on fly? This is critical to understand the effect of protein on DNA structural properties. I look forward to your reply. Best regards, Sarath ------------------------------ Message: 2 Date: Wed, 27 Dec 2017 21:39:41 +0700 From: Timofey Tyugashev <tyugas...@niboch.nsc.ru> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] More dihedrals generated than provided in the force field & "No default Proper Dih. types" as a result Message-ID: <86c9cd94-8371-5abc-db05-d469d17ae...@niboch.nsc.ru> Content-Type: text/plain; charset=utf-8; format=flowed I'm building a protein with a cubic [Fe4S4] cluster using parameters from a published paper. This parameters provide only two dihedral angles types (S-FE-SG-CB and FE-S-FE-SG, where S and FE belong to the cluster and SG and CB belong to the Cys residue). GROMACS automatically generates far more dihedrals with types like S-FE-S-FE (looks like all of them are inta-cluster) which are omitted in the source paper and are explicitly stated to be redundant for MD. However? grommp generates errors and stops: ERROR 49 [file topol.top, line 32916]: ? No default Proper Dih. types How to solve this problem? ------------------------------ Message: 3 Date: Wed, 27 Dec 2017 13:46:37 -0500 From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] More dihedrals generated than provided in the force field & "No default Proper Dih. types" as a result Message-ID: <c76426b1-eb96-3043-dfe9-5ff6fb800...@vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 12/27/17 9:39 AM, Timofey Tyugashev wrote: > I'm building a protein with a cubic [Fe4S4] cluster using parameters > from a published paper. > This parameters provide only two dihedral angles types (S-FE-SG-CB and > FE-S-FE-SG, where S and FE belong to the cluster and SG and CB belong > to the Cys residue). > GROMACS automatically generates far more dihedrals with types like > S-FE-S-FE (looks like all of them are inta-cluster) which are omitted > in the source paper and are explicitly stated to be redundant for MD. > However? grommp generates errors and stops: > > ERROR 49 [file topol.top, line 32916]: > ? No default Proper Dih. types > > How to solve this problem? pdb2gmx automatically generates all possible dihedrals. If they are not necessary in your force field description, either remove the offending lines from your topology or assign them dihedral parameters with force constants equal to zero so they impose no force. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== ------------------------------ Message: 4 Date: Wed, 27 Dec 2017 13:47:26 -0500 From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] regarding calculation of intra-residue energy Message-ID: <e69c5489-4b81-d9d5-53ac-243753149...@vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 12/26/17 1:34 PM, Saumyak Mukherjee wrote: > Dear all, > > I have simulated myoglobin in water system. Now, I want to calculate the > self interaction energy (Coulomb) of the protein. In that case shall I > consider the interaction between the OE1 and OE2 atoms in glutamte, or > other such pairs? > > Including all pairs, except the bonded pairs, the average self-energy of > the protein is coming as 8108 kT from my program. Is this value plausible? > > Any comment/suggestion is appreciated. First- and second-neighbor interactions are not included in standard force fields, so if your calculation includes them, you're going to get something that the force field is not designed to describe. Use the same exclusions as the force field expects. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== ------------------------------ Message: 5 Date: Wed, 27 Dec 2017 13:49:25 -0500 From: Justin Lemkul <jalem...@vt.edu> To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Osmotic Pressure Calculations and fixed reference values of walls Message-ID: <baa3845e-2ca5-61af-078c-a1f5fc7ad...@vt.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 12/26/17 7:53 AM, Mandar Kulkarni wrote: > Dear All, > I am performing osmotic pressure simulations using 30 nucleoside molecules > using 1D flat bottom restraints along Z-axis(Zmin and Zmax). I am using > GROMACS 5.0.7 version and reference coordinates are provided using -r > option in grompp. > The osmotic pressure runs are performed under NPT conditions with > semi-isotropic pressure coupling. I am calculating osmotic pressure using > C-program which simply calculates forces on heavy atoms of nucleosides > attempting to cross the Zmin and Zmax limits. > > I have searched archived posts, however, I am confused about possible > implementation and post-processing in the present case. Any help will be > really helpful to solve the following issues. > > 1. The upper and lower limits of the flat bottom restraints are defined > while starting the simulations using static reference frame. Although > |Zmax-Zmin| > will be constant, is it correct to assume fixed minimum(Zmin) and > maximum(Zmax) limits? Such calculations are usually performed with a static z-dimension, e.g incompressible along that axis. In that case, Zmin and Zmax are (and should be) fixed. > 2. During post-processing when one centers the trajectory and correct PBC > for nucleoside molecules (trjconv -pbc mol -ur compact -center options), is > it appropriate to assume the same Zmin and Zmax values at t=0 throughout > the analysis? You shouldn't have to use any complex trjconv command. Just make molecules whole and that should be correct. No additional centering is required; your molecules stay in the central volume anyway, and you don't want to shift coordinates when relying on fixed points in space for computing your osmotic pressure forces. -Justin > 3. The GROMACS source code section below calculates flat-bottom restraint > forces > > for (m = 0; (m < DIM); m++) > { > f[ai][m] += fm[m]; > /* Here we correct for the pbc_dx which included rdist */ > vir_diag[m] -= 0.5*(dx[m] + rdist[m])*fm[m]; > > } > > How can we print force f[ai][m] at each time step to separate file? I > assume it might be not straightforward to print these forces, but a short > general guideline might help me to achieve the objective. > > Sorry for so many questions and Thanks in advance. > Also, Wish you all happy new year in advance. > > Best Regards, > Mandar Kulkarni, > Pusan National University, South Korea -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== ------------------------------ Message: 6 Date: Wed, 27 Dec 2017 19:39:36 +0000 From: Diana Lousa <dlo...@itqb.unl.pt> To: Discussion list for GROMACS users <gmx-us...@gromacs.org> Subject: [gmx-users] Strange energy values with GMX 5.1, PME and Verlet Message-ID: <CANqofoxi85ABTWPJG=HqAXKOmRrBLyD3Myncj6eqbiP9P=5...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Dear all, For testing purposes, I performed a short simulation (10 ps) of a CL- and a Na+ ion in vacuum with gmx 5.1.4 and compared the Group and Verlet cutoff schemes. I ran gmx energy to monitor the interaction energy between the ions and obtained the following results: 1) Verlet Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------ ------------------- Pressure 0.128465 0.044 15.8209 -0.27251 (bar) Coul-SR:NA-NA -244.832 0 -nan -4.68375e-14 (kJ/mol) LJ-SR:NA-NA 0 0 0 0 (kJ/mol) Coul-SR:NA-CL -153.193 7.4 32.7214 -43.0706 (kJ/mol) LJ-SR:NA-CL 42.5252 1.7 20.9531 9.65428 (kJ/mol) Coul-SR:CL-CL -244.832 0 -nan -4.68375e-14 (kJ/mol) LJ-SR:CL-CL 0 0 0 0 (kJ/mol) 2) Group Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------ ------------------- Pressure 0.0159313 0.039 17.1949 0.303503 (bar) Coul-SR:NA-NA 0 0 0 0 (kJ/mol) LJ-SR:NA-NA 0 0 0 0 (kJ/mol) Coul-SR:NA-CL -152.361 8 33.2265 -46.2306 (kJ/mol) LJ-SR:NA-CL 42.2222 1.9 22.5877 11.0263 (kJ/mol) Coul-SR:CL-CL 0 0 0 0 (kJ/mol) LJ-SR:CL-CL 0 0 0 0 (kJ/mol) As you can see, the Coul-SR:NA-NA and Coul-SR:CL-CL have the value of -244.832 when using Verlet, which is very strange. This does not happen when using Group cutoff or when using Verlet in GMX 4.5 (the value is 0 in these cases). GMX 2016 gives similar results to GMX 5.1.4: 3) Verlet GMX 2016: Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------ ------------------- Pressure -0.0106255 0.22 19.2119 0.756146 (bar) Coul-SR:NA-NA -244.832 0 -nan -4.68375e-14 (kJ/mol) LJ-SR:NA-NA 0 0 0 0 (kJ/mol) Coul-SR:NA-CL -150.921 7.9 35.159 -45.7216 (kJ/mol) LJ-SR:NA-CL 42.0629 2 25.1668 11.2282 (kJ/mol) Coul-SR:CL-CL -244.832 0 -nan -4.68375e-14 (kJ/mol) LJ-SR:CL-CL 0 0 0 0 (kJ/mol) I am not using GPUs, since I know you cannot monitor energy groups when using GPUs. Does anyone have any idea why this happens and what consequences does it have? Here's the mdp: **************************** define = integrator = md tinit = 0.0 dt = 0.002 nsteps = 5000 nstcomm = 1 nstxtcout = 500 xtc-precision = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 10 nstenergy = 1 nstlist = 20 ns_type = grid ;PME rlist = 1.0 coulombtype = PME rcoulomb = 1.0 fourierspacing = 0.16 pme_order = 4 vdwtype = cut-off rvdw = 1.0 cutoff-scheme = Verlet ; or Group ; Energy monitoring energygrps = NA CL Tcoupl = v-rescale tc-grps = Ion tau_t = 0.10 ref_t = 300.0 ; Isotropic pressure coupling is now of ; Pcoupl = berendsen Pcoupl = No ; lincs_ constraint_algorithm=lincs lincs_order = 8 constraints = none lincs-warnangle = 90 ?Thanks in advance Best regards? -- Diana Lousa Post-doc Protein Modeling Laboratory ITQB/UNL Oeiras, Portugal ------------------------------ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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