[gmx-users] change the top file of a homodimer protein

of the topology file as follows? [ molecules ] ; Compound#mols Protein2 Thanks in advance, -- Qasim Pars -- 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

[gmx-users] restraint-lambdas and bonded-lambdas for binding free energy calculations

lambdas" and "bonded-lambdas" or one of them in the mdp files? - The dihedral_restraints and bonds under intermolecular_interactions aren't controlled by "restraint-lambdas" and "bonded-lambdas" in the mdp files, respectively, right? Thanks in adv

[gmx-users] edit dhdl.xvg file

. -- Qasim Pars -- 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

[gmx-users] about using restraint-lambdas and bonded-lambda

157.98 0.00.0157.980.0 41.840 1658 1656 2141 2140 1-123.02 0.00.0-123.020.0 41.840 1656 2141 2140 2136 1165.76 0.00.0165.760.0 41.840 Thanks in advance -- Qasim Pars -- Gromacs Users mailing list * Please search the archive

[gmx-users] Invalid order for directive atomtypes for ligands

; #ifdef POSRES #include "posre_LIG2.itp" #endif [ system ] Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 LIG1 1 LIG2 1 SOL16018 Thanks in advance -- Qasim Pars -- Gromacs Users maili

[gmx-users] how to set temperature-lambdas

is aim how should I set "temperature-lambdas" in the mdp file? simulated-tempering = yes sim-temp-low = 300 sim-temp-high = 450 simulated-tempering-scaling = linear temperature-lambdas=??? Any help will be appreciated. -- Qasim Pars -- Gromacs Users mailing list * Please search

[gmx-users] Contraints on both angles and dihedrals

Dear users, I would like to constraint all the angles and dihedrals of a ligand to make it rigid but Gromacs does not have this capability for the dihedrals. However, the angle and dihedral restraints do not make it rigid as I want, as it is very flexible. Do you have an idea on how I can

Re: [gmx-users] Slowly changing the q and vdw interactions for free energy calculations

Hi, Any comments on my questions? > On 3 May 2018, at 19:48, Qasim Pars <qasimp...@gmail.com> wrote: > > Dear users, > > For the binding free energy calculations I would slowly first turn off the > coulomb interactions, and then the vdw interactions at only one pr

[gmx-users] Slowly changing the q and vdw interactions for free energy calculations

Dear users, For the binding free energy calculations I would slowly first turn off the coulomb interactions, and then the vdw interactions at only one production step of 1 ns (not multiple simulations as in MBAR). My questions are: Can I do that with gromacs? I don't know whether the following

[gmx-users] degrees of freedom and position restraint

Dear users, I am confused about the position restraints. My questions are here: Q1: if I apply the position restraints (define = - DPOSRES) on the system in the production run step whether or not I will loose the translational, rotational and vibrational freedom resulting in an entropy

[gmx-users] using constant velocities during simulation

Dear users, I would like to use the constant velocities for all the atoms of both protein and ligand during all the simulation steps (EM, NVT, NPT and MD). Do you know how I can do that with GROMACS? In this case, the COM, the linear momentum and angular momentum of both groups wouldn't change

Re: [gmx-users] Perturbing Proteins

Hi, Good question! The nstcomm is the frequency at which the center of mass motion is removed. My guess is that using short frequency for the nstcomm (e.g. nstcomm=1 while simulation time step is 1 fs, dt=0.001) can perturbe the system. That is, the system may not return to its

[gmx-users] Software inconsistency error with version 2016.1

238) MPI rank:23 (out of 32) Software inconsistency error: Some interactions seem to be assigned multiple times Any help will be appreciated. -- Qasim Pars -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

Re: [gmx-users] domain decomposition error in the energy minimization step

Don't forget to check your simulation performance, there will >be better and worse choices in terms of these decomposition parameters. > > Happy simulating! > Carsten > > > > On 11 Jan 2017, at 08:33, Qasim Pars <qasimp...@gmail.com> wrote: > > > >

[gmx-users] domain decomposition error in the energy minimization step

.mdp and [ intermolecular_interactions ] section in the top file but GROMACS still gives the domain decomposition error for the complex structure. Will you please give suggestions on getting rid of the lincs warning and domain decomposition messages? I would appreciate any kind of help. Thanks. -- Q

Re: [gmx-users] couple-intramol

Hi, Thanks. If I want to calculate the intramolecular energy of the ligand, I need to choose Coul-14:LIG-LIG, LJ-14:LIG-LIG, Coul-SR:LIG-LIG and LJ-SR:LIG-LIG in the .edr file. Am I wrong? On 4 January 2017 at 04:03, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/3/17 2:40

[gmx-users] couple-intramol

mbda0 = vdw-q couple-lambda1 = none nstdhdl = 100 Thanks in advance, -- Qasim Pars -- 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.gro

[gmx-users] forward and backward states for the binding free energy energy

B parameters to the [ intermolecular_interactions ] parts. That should be enough to define the state B of a molecule in GROMACS2016? Thanks in advance. Qasim Pars -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

[gmx-users] free energy settings

to be a residue of the protein, and there is not need to have a state B defined in the topology file, as the couple- flags in the mdp already build the B state for the decoupled ligand automatically. Am I wrong? Thanks in advance -- Qasim Pars -- Gromacs Users mailing list * Please search

[gmx-users] pmf settings

of mass of each group? Hope someone will answer the questions. Cheers, -- Qasim Pars -- 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

[gmx-users] pull code and binding free energy

to use [ bonds ] under [ intermolecular-interactions ] in the topology file? Third question: The PMF or the binding free energy (alchemical) is the best one to calculate free energy? And why? Any answer will be greatly appreciated. Cheers, -- Qasim Pars -- Gromacs Users mailing list * Please

Re: [gmx-users] binding free energy with gromacs2016

Dear users, Hope someone will answer the questions in my previous mail. Thanks in advance, > On 6 Nov 2016, at 23:48, Qasim Pars <qasimp...@gmail.com> wrote: > > Dear users, > > I will try to do binding free energy calculation using GROMACS2016 but I am > con

[gmx-users] binding free energy with gromacs2016

ROMACS2016 manual but I couldn't understand how to prepare the input files. -- Qasim Pars -- 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

Re: [gmx-users] least-squares fitting the second structure on the reference structure

on each other's. Cheers, On 23 June 2016 at 00:14, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Qasim, > > If you fit a trajectory, with trjconv -fit rot+trans, then each frame is > fit onto the reference. > > Hope it helps, > > Tsjerk > > On Tue, Jun 21,

[gmx-users] least-squares fitting the second structure on the reference structure

Dear users, >From GROMACS online manual: gmx confrms computes the root mean square deviation (RMSD) of two structures after least-squares fitting the second structure on the first one. My question is how GROMACS does least-squares fitting the second structure (each frame of trajectory) on the

Re: [gmx-users] Insufficient memory (128 GB) for ensemble entropy calculation with gmx covar/gmx anaeig

Dear David, Could you please more explain each term of the formula you said? Formula=The number of atoms (N * 3)^2 times number of frames times 4 bytes Why square the number of atoms? Why 4 bytes? Thanks in advance > On 21 Jun 2016, at 09:39, David van der Spoel wrote:

[gmx-users] to neutralize the system

haven't come across with any problems because of the charge of the system. It means that the PME method works at a charged complex system properly. In spite of that, do you think that I need to neutralize a charged complex system? Can anyone comment on above questions? Cheers, -- Qasim Pars

Re: [gmx-users] Saving time of the coordinates for conformational entropy

f it goes above > 0.5 nm. > > Cheers, > > Tsjerk > > >> On Wed, Jun 8, 2016 at 8:48 PM, Qasim Pars <qasimp...@gmail.com> wrote: >> >> Dear users, >> >> I have simulated a protein with simulation time of 200 ns and saving the >

[gmx-users] Saving time of the coordinates for conformational entropy

Dear users, I have simulated a protein with simulation time of 200 ns and saving the coordinates at every 40 ps. Conformational entropy (~4500 kJ/mol K) obtained by Quasiharmonic approach using gmx covar and gmx anaeig tools is not consistent with literature (~2500 kJ/mol K). Whereas, the RMSD

[gmx-users] distance between two groups

the distance between ligand and each residue as a function of time. Cheers, -- Qasim Pars -- 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

Re: [gmx-users] projection on the first two eigenvectors obtained from the concatenated trajectories

in the preparation, the execution and the interpretation. > Please do read plenty of tutorial material dealing with it, not only from > the perspective of simulations, but also from the linear algebra view. > > Cheers, > > Tsjerk > > On Tue, Jun 7, 2016 at 2:09 PM, Qasim Pars <qasimp...@gma

[gmx-users] projection on the first two eigenvectors obtained from the concatenated trajectories

eigenvec.trr -2d two-ligands.xvg -first 1 -last 2 Cheers, -- Qasim Pars -- 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

Re: [gmx-users] Cross correlation map of residues

;> Hi Qasim, >> >> The plot you refer to is the result of NMA on C-alpha only. So g_covar >> -xpma using only C-alpha atoms should come close. You might also want to >> try the g_correlation tool mentioned earlier on the list, but again with a >> selection of on

Re: [gmx-users] allosteric effect

MD for this and would be interested in > people's views. > > Best wishes > James > > > Hi Qasim, > > > > Do you assume MWC or KNF like allostery, and conformational based, > > dynamics > > based or mixed? > > > > Cheers, > > >

[gmx-users] allosteric effect

, in advance. -- Qasim Pars -- 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

[gmx-users] Cross correlation map of residues

for each atom pair but it is not what I want. Any suggestions will be appreciated. -- Qasim Pars -- 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