Re: [gmx-users] continue simulation from intermediate frame instead of last frame

1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 Thanks for your replies. I appreciate it. On Wed, Oct 4, 2017 at 3:07 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/4/17 9:06 AM, tarak karmakar wrote: > >&

[gmx-users] continue simulation from intermediate frame instead of last frame

Hi All, Is there any way to continue a simulation from an intermediate time scale, (say, from a frame at time=180 ns instead of 190.772 ns)? gmx_mpi_d convert-tpr -s topol.tpr -f state_prev.cpt -e ener.edr -time 18 -o topol.tpr gmx_mpi_d mdrun -s topol.tpr -noappend This does not help as it

Re: [gmx-users] Open-closed transition in a dimeric enzyme, WTM simulations

rections. This can > be difficult to know beforehand unfortunately. > > Kind regards, > Erik > > > On 10 Jun 2016, at 19:09, tarak karmakar <tarak20...@gmail.com> wrote: > > > > Dear All, > > I am studying an enzyme where the closing of a loop should happen upon

[gmx-users] unusual behavior of CV in steered MD (gromacs+plumed)

Dear All, I am running a SMD simulation (gromacs+plumed) pulling a ligand out of the enzyme. The parameters are, pulling velocity= 0.5 per 1000 steps (2 ps, as in gromacs) force constant = 20920.0 kJ/mol/nm-2 CV from 0.3 nm to 1.7 nm STEER CV 1 FROM 0.3 TO 1.7 KAPPA 20920.0 VEL 0.5 So, I

[gmx-users] Open-closed transition in a dimeric enzyme, WTM simulations

Dear All, I am studying an enzyme where the closing of a loop should happen upon ligand binding to the active site. In unbiased simulations, even after 300 ns of simulation time the loop does not close the reaction center. Thus, we realized that the open-closed conformational change may have a

[gmx-users] AMBER99SB and gaff X OS P X dihedral parameters

Dear All, I have a confusion related to two dihedral parameters that are present in ffbonded.itp file, X OH P X 9 0.0 1.04600 3 ; JCC,7,(1986),230 X OS P X 9 0.0 1.04600 3 ; JCC,7,(1986),230 the similar dihedral parameters from parm99SBgaff.dat

[gmx-users] Plumed-2.2.0 installation issue

Dear All, Lately, I am trying to install Plumed-2.2.0 in one system, the steps I follow, ./configure prefix=/home/tarak/software/plumed-2.2.0 CXX=mpicxx make install Config.log shows no error, but while giving "make install" it is coming out of the process with the following errors,

[gmx-users] RB dihedral type in amber99sb-ildn ffbonded.itp

Dear All, I need to impose a distance restraints between COM of protein active site residues and COM of a ligand. But the problem is I am using an .itp file generated from acpype. While I use the ligand.itp externally, I can not impose the distance restraints between the protein and the ligand.

Re: [gmx-users] Dihedral copying from itp to ff

Dear Justin and Mark, I also need to impose a distance restraints between COM of protein active site residues and COM of a ligand. But the problem is I am using an .itp file generated from acpype. While I use it externally I can not impose the distance restraints between the protein and the

Re: [gmx-users] (no subject)

Hi PAULAMI, Use gmx trjcat to concatenate the two trajectory files and then calculate the rmsd. http://manual.gromacs.org/programs/gmx-trjcat.html Best wishes, Tarak On Thu, Jul 9, 2015 at 1:34 PM, PAULAMI CHATTERJEE chatterjee_paul...@yahoo.co.in wrote: Dear All, I have a 30 ns trajectory

Re: [gmx-users] Adding missing heavy atoms

Hi Prasun, If you really want to prepare the structure of a molecule, better try any modelling software. GaussView could be a handy option. Export your molecule in .pdb format and a little bit of modification will make your nucleotide ready to use. Best wishes, Tarak On Sat, Jul 11, 2015 at

[gmx-users] entropy calculation

Hi Prof. David van der Spoel and Dr. Lemkul, We had quite an interesting discussion related to the entropy calculation in gromacs-4.5 version. Lately, I resumed the configurational entropy calculations in the newer (not latest) version of gromacs. Presently, I am looking into the results of a

[gmx-users] Distance restraints

Dear All, I'm trying to keep distance restraints between few atoms, and for that I have done the following, In the topology file, I have inserted a block specifying the details of pairs -- ; Include forcefield

Re: [gmx-users] Semiisotropic pressure coupling

Hi All, Just read the thread and got some new information. I'm currently simulating a pure DPPC bilayer with charmm36 lipid parameters in gromacs-5.0.4. In doing so, I got a lower area per lipid (~0.56 nm^2) compared to the experimental one (~0.63nm^2). The trajectory has run for ~3-4 ns. I have

Re: [gmx-users] lower Area per lipid for DPPC with CHARMM36

/no) -- Any suggestion would be helpful. Thanks, Tarak On Mon, Feb 16, 2015 at 4:01 PM, tarak karmakar tarak20...@gmail.com wrote: Oh! Thanks. :) Sorry I should have checked it before running

Re: [gmx-users] lower Area per lipid for DPPC with CHARMM36

Oh! Thanks. :) Sorry I should have checked it before running the simulation. Now, I'm getting APL ~62.5 A^2 which is pretty good compared to the expt. On Sun, Feb 15, 2015 at 6:28 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/15/15 7:39 AM, tarak karmakar wrote: Dear All, All atom

Re: [gmx-users] Peptide-membrane simulation force field parameters

:28 AM, tarak karmakar wrote: Dear All, I need a suggestion related to simulation of peptide-membrane system. Are CGenFF parameters (from ParamChem) for peptide analogues good enough to couple with Charmm36 parameters for the lipids in a membrane? (provided very low charge and param penalties

[gmx-users] lower Area per lipid for DPPC with CHARMM36

Dear All, All atom simulation of DPPC bilayer (128 lipids) is resulting a low area per lipid (sliding down from ~58 to ~54 in 4 ns NPT). I'm performing the simulation in gromacs-5.0.4 with the charmm36 force field parameters for the lipid molecules. The NPT.mdp is pasted bellow,

[gmx-users] Peptide-membrane simulation force field parameters

Dear All, I need a suggestion related to simulation of peptide-membrane system. Are CGenFF parameters (from ParamChem) for peptide analogues good enough to couple with Charmm36 parameters for the lipids in a membrane? (provided very low charge and param penalties) Thanks, Tarak -- Gromacs Users

[gmx-users] Projection of trajectory onto PCs

Dear All, Could anyone please elaborate 'projections of trajectory onto first two principal components' in PC analysis? Projection of trajectory onto first two eigenvectors- Does it mean that i) the superposition of molecular structures (a set of C-alpha coordinates) over a trajectory are

Re: [gmx-users] entropy vs time plot

Dear Sir, Thanks for the piece of script. Bit modification and it works superbly. thanks, Tarak On Wed, May 21, 2014 at 1:23 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2014-05-21 06:54, tarak karmakar wrote: Hi Tsjerk, Thanks for the quick reply. I did the following g_covar

[gmx-users] Schlitter Configurational entropy 'NaN'

Dear All, I wanted to calculate configurational entropy of a protein by using g_covar and g_anaeig as follows, g_covar -f ../traj.xtc -s ../npt_prod -o eigenval -v eigenvec.trr -av average.pdb g_anaeig -v eigenvec.trr -entropy -temp 300 I got the following results The Entropy due to the Quasi

Re: [gmx-users] Schlitter Configurational entropy 'NaN'

: On 2014-05-15 09:07, tarak karmakar wrote: Dear All, I wanted to calculate configurational entropy of a protein by using g_covar and g_anaeig as follows, g_covar -f ../traj.xtc -s ../npt_prod -o eigenval -v eigenvec.trr -av average.pdb g_anaeig -v eigenvec.trr -entropy -temp 300 I got

Re: [gmx-users] Entropy

Hi Yulian, I've also faced the same problem. In different machine the value is coming different. Which method did you use to calculate entropy? QH or Schlitter? In my case Schlitter is giving 'nan'. Did you solve your problem after then? If so, please suggest me how to deal with this. Tarak

Re: [gmx-users] Schlitter Configurational entropy 'NaN'

interesting that the code printed 'nan' after 999 th term. What does this mean? Is there any upper limit of number of atoms (c-alpha here)? Tarak On Thu, May 15, 2014 at 2:54 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2014-05-15 10:51, tarak karmakar wrote: | Is your system far

Re: [gmx-users] Schlitter Configurational entropy 'NaN'

= 0 hwkT =inf dS = -nan So, there is precision problem in the code; 10^-16 is taken as zero!! Tarak On Thu, May 15, 2014 at 5:23 PM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2014-05-15 11:40, tarak karmakar wrote: Dear Sir, Thank you again for guiding me towards

Re: [gmx-users] Schlitter Configurational entropy 'NaN'

wrote: On 2014-05-15 18:41, tarak karmakar wrote: Hi Justin, That's true and it is a C code and 0 index loop. Then the strange jump 999 to 1000 came in to the picture. But what about dealing with very small numbers? What does g_covar print? It seems the problem might be there, because

Re: [gmx-users] MM-GB/SA analysis in Gromacs

Dear Andrea, I've simulated a protein dimer for a long time span and now I need to perform MM-PBSA calculations to get the binding free energy between the two monomers. Could you please send me the script to carry out this calculation. I've read your paper Exploring PHD Fingers and H3K4me0

[gmx-users] Protein-protein interaction energy

Could anyone guide me to analyze protein-protein interaction energy in a MD trajectory? I'm simulating a dimer and want to see the interaction energy between the two monomers. Is it the same way like specifying the two chains (say residues 1-100 and in the other monomer

[gmx-users] Ryckaert-Bellemans Dihedral with AMBER

Dear All, I need to use one Ryckaert-Bellemans dihedral type of a dihedral in a new molecule. To do so, I'm including all the coefficients in .rtp file as given below, (after bonds section) [dihedrals] HX CXCX OX3 -7.70990 -10.7269 -15.2261 -2.2442 -0.25839 0. The Force

Re: [gmx-users] Ryckaert-Bellemans Dihedral with AMBER

...@vt.edu wrote: On 3/26/14, 1:30 PM, tarak karmakar wrote: Dear All, I need to use one Ryckaert-Bellemans dihedral type of a dihedral in a new molecule. To do so, I'm including all the coefficients in .rtp file as given below, (after bonds section) [dihedrals] HX CXCX OX3

Re: [gmx-users] problem with tutorial KALP-15 in DPPC

step 0: Water molecule starting at atom 101831 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. I would suggest you to do one more round of minimization by taking the final minimized .gro file and then perform a short simulation with a time step of 0.5 fs.

Re: [gmx-users] Simulate Lennard-Jones System

manual 4.1.1 (gromacs-4.5.5) On Fri, Jan 31, 2014 at 11:06 AM, Zhikun caiz...@gmail.com wrote: Dear users, I would like to simulate a Lennard-Jones system with one or two species of atoms. But my knowledge is only about Lennard-Jones 6-12 potential and I haven't figured out how to use that

Re: [gmx-users] pbc problem

Hi, trjconv -s topol.tpr -f traj -pbc mol -o traj_modified select '0' for the entire system You can try using either 'mol' or 'nojump' depending on your visualization needs. cheers, Tarak On Wed, Jan 29, 2014 at 3:39 PM, Atila Petrosian atila.petros...@gmail.comwrote: Dear Gromacs users I

Re: [gmx-users] How to visualize the Free Energy Landscape file generated by g_sham

Hi Monoj, You can use GNU 3D plot for this particular case. cheers, Tarak On Wed, Jan 29, 2014 at 8:02 AM, Monoj Mon Kalita mon.123c...@gmail.comwrote: Dear Gromacs user, I have used the g_sham method to generate free-energy-landscape.xpm file. To do that I have followed this website

[gmx-users] Plumed-2 WTMetadynamics PBC

Dear All, I'm running a Well-Tempered Metadynamics simulation of gate opening and ligand release of a protein in gromacs-4.5.5 patched with plumed-2. Plumed.dat file is given below COM ATOMS=1848-2074 LABEL=L1 COM ATOMS=3141-3329 LABEL=L2 DISTANCE ATOMS=L1,L2 LABEL=gate_width COM

Re: [gmx-users] g_helix segmentation fault grom-4.6.5

the situation, but if a developer isn't using a tool, it doesn't get any love! Are you trying to say it doesn't work in 4.6.5? Mark On Jan 16, 2014 5:51 AM, tarak karmakar tarak20...@gmail.com wrote: Dear All, Bit confused with the g_helix utility in gromacs-4.6.5. I've simulated a membrane protein