[gmx-users] Rotation of single moleculae in vacuum

I simulate a single flexible molecule with no PBC starting from its optimized configuration (L_BFGS) and immediately turning T-coupling on. >From the very beginning, the molecule starts to rotate around COM. Although this motion may not matter for an isolated molecule, I'd be happy to understand a

[gmx-users] Free energy: sum or average

Upon free energy calculations via continuous decoupling, free-energy = yes couple-moltype = MOL couple-lambda0 = vdw-q couple-lambda1 = none couple-intramol = no init-lambda = 1.0 delta-lambda = -4e-8 sc-alpha

Re: [gmx-users] NPT equilibration with small cell

you are on the right way. set high pressure. set cut-offs to half box side. run classical MD, ~10 000 steps, and, afterwards, manually increase the box sides to mimic the experimental density in the plane-wave DFT, run local optimization prior to AIMD. On Tue, Feb 16, 2016 at 4:01 PM,

Re: [gmx-users] how to modify the code to generate more controllable checkpoints to restart?

I suppose the TRR file, which you can write down at given frequency, contains the same information with the same precision as it is written down to the CPT file. On Tue, Jan 26, 2016 at 7:50 AM, Yong Wang wrote: > Hi, > > I'd like to restart the MD simulation from some

Re: [gmx-users] Temperature or Pressure Coupling

yes On Tue, Jan 26, 2016 at 3:42 AM, sun wrote: > Hello > I want to simulate a protein in water and observe its behavior alone and > then in the presence of ligand. I have read somewhere that NPT MD is best > for pro-lig complexes as it resembles the in vitro and in vivo

Re: [gmx-users] how to modify the code to generate more controllable checkpoints to restart?

osing nsteps, save that checkpoint > > file, > > > and then continue. That's slightly wasteful of computer time, doing > extra > > > shut-down and start-up work, but you can have it working in five > minutes > > > ;-) > &

[gmx-users] Surface tension: output units

What are the units of surface tension derived thru g_energy? I am confused with the header: (kJ mol\S-1\N) -- 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] Energy profile of a single water molecule on Ni surface

On Sat, Jan 23, 2016 at 12:16 PM, Alexander Alexander < alexanderwie...@gmail.com> wrote: > Dear Gromacs user, > > I am a new user trying to produce the energy profile of a single water > molecule on Ni(111) surface, I mean adsorption energy of water molecule on > surface VS the distance of the

Re: [gmx-users] Membrane simulation npt problem

/gen/2016 03:42, "VITALY V. CHABAN" <vvcha...@gmail.com> ha scritto: > >> The problem is outside your parameter file. >> >> >> >> >> >> On Fri, Jan 15, 2016 at 3:56 PM, Marco Franzoi <marco.franzo...@gmail.com >> > >> wr

Re: [gmx-users] how to maintain planarity of graphene sheet

et the topology file (even for part of) the graphene , it > would have been very helpful. I could have replicated and improvised the > topology files for the graphene size I am interested in. > Jagannath > > On Fri, Jan 15, 2016 at 6:14 AM, VITALY V. CHABAN <vvcha...@gmail.com&

Re: [gmx-users] Membrane simulation npt problem

The problem is outside your parameter file. On Fri, Jan 15, 2016 at 3:56 PM, Marco Franzoi wrote: > Good evening to everyone. > > I've an issue regarding a membrane simulation. > I've downloaded an already equilibrated POPE/POPG membrane and, to test the > system,

Re: [gmx-users] how to maintain planarity of graphene sheet

By using high force constants for all bonded terms. An ideally planar graphene in the solution/dispersion is an unphysical model though. You must read literature for further insights: http://pubs.rsc.org/en/content/articlelanding/2015/ra/c5ra16857k#!divAbstract On Thu, Jan 14, 2016 at 5:13

Re: [gmx-users] g_dipoles_mpi

I vaguely recollect that this stuff works in 4.0.7 and, likely, all earlier versions. On Mon, Jan 11, 2016 at 9:19 PM, ayşe K wrote: > Dear Gromacs Users, > > Some options do not run while I'm doing calculations by the programs of > gromacs. > > For example, I

Re: [gmx-users] how to maintain planarity of graphene sheet

bonds, angle and dihedrals ? > Jagannath > > > > On Thu, Jan 14, 2016 at 6:53 PM, VITALY V. CHABAN <vvcha...@gmail.com> > wrote: > >> By using high force constants for all bonded terms. >> >> An ideally planar graphene in the solution/dispersion is an unp

Re: [gmx-users] viscosity using green kubo relation for ionic liquids

EqMD methods work poorly for highly and moderate viscous liquids. On Tue, Jan 12, 2016 at 5:19 PM, shanmuga sundaram wrote: > I tried with g_energy -vis , but it calculates using einstein relation. I > want to calculate using green kubo equation. > > > regards, > >

Re: [gmx-users] genion with Na or Ca

Ca(2+) will block one of your binding sites, if you care. On Tue, Jan 12, 2016 at 6:19 AM, Turgay Cakmak wrote: > Hi all, > > > I have a quick question about neutralizing the system. I have a solvated > system that contains a charged protein of -2q. Is there a

Re: [gmx-users] bond constraints: which distance is constrained?

ok thank you On Wed, Dec 16, 2015 at 11:33 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 12/16/15 8:29 AM, Vitaly V. Chaban wrote: > >> In bond constraints (all-bonds; LINCS...), does it constrain an initial >> bond length (as in GRO) or an equilibrium bon

[gmx-users] bond constraints: which distance is constrained?

In bond constraints (all-bonds; LINCS...), does it constrain an initial bond length (as in GRO) or an equilibrium bond length (as in ITP)? My tests reveal the constrained distance is taken from ITP, which is somehow counter-intuitive to me. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] supervised MD in Gromacs?

The only thing you need is to arrange the existing gromacs utilities into a script. Python, Perl, Bash languages do this very well. P.S. It is not very honest of the algorithm authors to call it *unconstrained* while they simply disregard motions that they do not like. On Tue, Dec 8, 2015 at

Re: [gmx-users] RDF convergence

Mine converges. What about box size? On Fri, Dec 4, 2015 at 7:14 AM, Sudip Das wrote: > Hi, > > I am using g_rdf command (within gromacs-5.0.5) to calculate rdf as follow: > > g_rdf_mpi_d -f .xtc -n .ndx -o rdf -cn > > But the rdf is not getting converged to 1

Re: [gmx-users] creating an "infinite" filament with editconf

Perhaps, it is technically easier to freeze the boundary atoms along the periodic direction. On Mon, Dec 7, 2015 at 9:26 AM, David van der Spoel wrote: > On 07/12/15 11:54, Igaev, Maxim wrote: > >> Dear Gromacs Users, >> >> I have a protein dimer and would like to make

Re: [gmx-users] xtc files

gromacs does not support "spherical" boxes, as well as I do not think this would have been correct in view of PBC. No PBC will eventually lead to the spherical cluster representation. On Mon, Dec 7, 2015 at 10:07 AM, mihammad roos wrote: > Hello everybody, > > >

Re: [gmx-users] Methanol geometry parameters

You, perhaps, need to care about *compatibility* of this old methanol and your solute molecule. On Thu, Dec 3, 2015 at 2:08 PM, Peter Stern wrote: > The force field parameters are defined in ffbonded.itp and ffnonbonded.itp. > You still need starting coordinates

Re: [gmx-users] energy autocorrelation function: bug?

iof...@gmail.com> wrote: > Dear Vitaly, > > I usually compute the ACF with the funtion g_analyze. > > I hope it helps. > > Cheers, > Mario > > 2015-11-11 14:26 GMT+01:00 Vitaly V. Chaban <vvcha...@gmail.com>: > > > I compute the energy ACF by using >

[gmx-users] energy autocorrelation function

I compute the energy ACF by using g_energy_mpi -fluc -corr However, no ACF is present in the output. Only energy.xvg is created with one column of data, which are obviously not ACF. The version is 5.0.4. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Fwd: NVT to NVE ensemble, energy drifting problem

Decrease the time-step. On Tue, Nov 3, 2015 at 3:00 PM, gozde ergin wrote: > -- Forwarded message -- > From: gozde ergin > Date: Tue, Nov 3, 2015 at 5:39 PM > Subject: NVT to NVE ensemble, energy drifting problem > To: mailing

Re: [gmx-users] Flat-bottomed potential from user-defined reference

Gromacs uses restraints to keep molecules near their original positions. See the manual. On Tue, Nov 3, 2015 at 8:24 AM, Cosseddu, S.M. wrote: > Dear all, > > I am trying to apply a spherical flat-bottomed potential to maintain some > molecules within a certain region. By

Re: [gmx-users] implicit solvent with periodic molecules

Yes. It is formally possible. I do not think that implicit solvation precludes PBC usage. On Thu, Oct 29, 2015 at 9:40 AM, Анна Павловна Толстова < tolst...@physics.msu.ru> wrote: > Hello, gmx_users. > > Is that possible to simulate a protein adsorption on graphite sheet with > implicit

Re: [gmx-users] Dihedral Coeffecient Conversion

You plot the function; you fit the curve with another equation; you write down the coefficients. Most electronic-tables tool makes the job. That's it. On Tue, Oct 27, 2015 at 12:23 PM, Mark Abraham wrote: > Hi, > > The manuals document the functional forms in

Re: [gmx-users] combining OPLS Protein and Berger Lipids

Strictly speaking, whatever you combine is wrong, because the Berger FF uses hand-adjusted parameters in view of experimental data, while OPLS does not. Therefore, the inter-molecular Berger-OPLS parameters are incorrect, both the weak part and the electrostatic part, since Berger akyl chains do

Re: [gmx-users] Viscosity calculation by g_tcaf

On Sat, Oct 24, 2015 at 5:31 AM, Pallavi Banerjee < pallavis...@students.iiserpune.ac.in> wrote: > Hello Users, > > Does the viscosity obtained from g_tcaf depend on the system size or the > interval of recording trajectory or both? What is considered to be the > ideal frequency of recording

Re: [gmx-users] Lennard Jones parameters for Sp, Sp2 and Sp3 nitrogen identical?

Likely because the LJ constants of N are less important to reproduce the correct structures of organic molecules and their phases. Also, there are probably not so many strong coordination patterns involving N, which are practically important. On Thu, Oct 22, 2015 at 1:04 PM, Ebert Maximilian

Re: [gmx-users] Temperature output file

Temperature groups have to be defined in the parameter file to derive the coveted data, I believe. On Thu, Oct 22, 2015 at 11:05 AM, Justin Lemkul wrote: > > > On 10/22/15 9:01 AM, Ali Mohyeddin wrote: > >> Dear all, >> >> I am very beginner to gromacs. I have already

Re: [gmx-users] suspension of colloids in GROMACS

On Thu, Oct 22, 2015 at 12:17 PM, CARDELLINI ANNALISA wrote: > Dear gromacs users, > In one project, I have to do some coarse grained molecular dynamics (CGMD) > simulations of nano-colloids (inorganic particles 100-150 nm, 3%wt max very > dilute) by using soft potentials

Re: [gmx-users] acceptable errors in density and melting point

Density discrepancy of 12% is unacceptable for any substance. Melting point is better, if T is in K. Different properties assume different healthy discrepancy thresholds. On Thu, Oct 15, 2015 at 6:02 PM, Victor Rosas Garcia wrote: > Thanks Justin. That's what I

Re: [gmx-users] Normal Mode Analysis

Perhaps, trjconv -- to delete all you do not need? On Wed, Oct 14, 2015 at 2:49 PM, Dan Sponseller wrote: > Hello. > > I am trying to do a Normal Mode Analysis of a polymer in water. I am > running my minimization right now with -DFLEXIBLE defined. > > How do I exclude

Re: [gmx-users] Artificial Restraint/Wall/Potential at box top

Is it not better to post-process the trajectory, trjconv, to obtain the bilayer where you need it? Restraints impact the simulation results and this impact is not always easy to isolate. On Wed, Oct 14, 2015 at 3:34 PM, Mark Abraham wrote: > Hi, > > You may want to

Re: [gmx-users] simulating Cellulose using GAFF force field

Plot all energy components vs. time. Normally, the probem is within dihedrals, e.g. not all of them defined. On Mon, Sep 21, 2015 at 11:17 AM, Fahimeh wrote: > Hi gromacs users, > > I am trying to melt a crystalline structure of cellulose. This structure >

Re: [gmx-users] K+ ions instead of NA+ for neutralization

Perhaps, K+ is even better. On Sun, Sep 13, 2015 at 4:10 AM, Andrew Bostick wrote: > Dear gromacs users, > > For neutralizing the simulation system, can I use K+ ions instead of NA+? > > Best, > Andrew > -- > Gromacs Users mailing list > > * Please search the

Re: [gmx-users] NVE+NVE: Two groups: one with Tcouple while the other one not

he Tcoupl for nC12 (by setting tau_t = -1). What > would be reasons? > > ---------- > *From: *"Vitaly V. Chaban" <vvcha...@gmail.com> > *To: *"gmx-users" <gmx-us...@gromacs.org> > *Sent: *Thursday, September 10, 2015 8:37:52 PM >

Re: [gmx-users] topology parameters

Bonded interactions are important. Sections are for human understanding. On Sun, Sep 6, 2015 at 3:36 AM, mah maz wrote: > Dear users, > > Are resnr, residue, moleculetype, system and molecules names in .top file > important? I have a CNT containing water molecules. I can

[gmx-users] g_angle and a dihedral

I compute a dihedral using g_angle. g_angle -h: It should be noted that the index file must contain atom triplets for angles or* atom quadruplets for dihedrals*. If this is not the case, the program will crash. I get: Program g_angle_mpi, VERSION 4.6.1 Source code file:

Re: [gmx-users] Force field selection for free Bicarbonate molecules in solution

My group works with the bicarbonate and similar anions in the context of CO2 chemisorption. You must exercise serious caution to assign correct electrostatic potential at the surface of the anion and account for hydration/solvation effects within the force field derivation procedure. On Fri,

Re: [gmx-users] Heating step by step.

annealing-time: 0.000 0.001 5.000 5.001 10.000 10.001 15.000 annealing-temp: 0 20 20 40 40 60 60 However, your simulation schedule makes little sense physically . Remember that what you change here of the thermostat's reference temperature,

Re: [gmx-users] extend a simulation just with xtc file

trjconv -dump $last_frame -o conf.gro grompp -c conf.gro This will allow you to restart the simulation, if you do not care about an exact continuation of the phase space trajectory that you probably do not. On Wed, Sep 2, 2015 at 10:51 AM, Adriana Garro wrote: >

Re: [gmx-users] OPLS/AA parameters for 2-propanol

Normally, this sort of things is done via mechanical combining of the known groups -- CH3, -CH, OH -- from the force field. If your goal is to increase accuracy for pure 2-propanol per se, then play with the distribution of electronic density between OH and CH. If 2-propanol is to be used as a

Re: [gmx-users] OPLS/AA parameters for 2-propanol

Max > >> On Sep 2, 2015, at 2:08 PM, Vitaly V. Chaban <vvcha...@gmail.com> wrote: >> >> Normally, this sort of things is done via mechanical combining of the >> known groups -- CH3, -CH, OH -- from the force field. >> >> If your goal is to increase accu

Re: [gmx-users] NVE Vacuum Fluctuation of Energy

The major source is rounded numbers -- in all functions, not only in the motion propagation algorithm. On Tue, Sep 1, 2015 at 11:20 PM, Johnny Lu wrote: > Dear Users, > > I was trying to run NVE simulation of alanine peptide in vacuum with double > precision gromacs

Re: [gmx-users] Green Kubo viscocity calculation

Try 5-20fs. On Wed, Sep 2, 2015 at 12:06 AM, Aishwary Shivgan <aishwaryshivga...@gmail.com> wrote: > Currently I saving the energies after every 50 fs. Should I decrease more? > On Sep 2, 2015 3:23 AM, "Vitaly V. Chaban" <vvcha...@gmail.com> wrote: > >

Re: [gmx-users] charge neutralization in vacuum simulations

To get a neutral protein, protonate all residues... Another question is what's your simulation goal, since protonated and deprotonated residues behave obviously in a different way. On Tue, Sep 1, 2015 at 6:57 AM, tasneem kausar wrote: > Dear Gromacs users > > I am

Re: [gmx-users] Unusual Blow up

Reduce the time-step. On Tue, Sep 1, 2015 at 10:40 AM, Nima Soltani wrote: > Hi everyone > I am simulating the interactions between a small peptide and different > metallic surfaces solvated in TIP3P water. > So far i have simulated 3 different surfaces correctly ,

Re: [gmx-users] Green Kubo viscocity calculation

ulation? > I tried > g_energy -vis > g_analyze -f visco.xvg > it's giving me viscosities 10 times higher than actual. > > On Sun, Aug 30, 2015 at 2:11 AM, Vitaly V. Chaban <vvcha...@gmail.com> > wrote: >> >> g_energy -vis >> g_analyze -f visco.xvg >

Re: [gmx-users] simulations of ice beginning to spin

I need anything in my input file? Thanks, Nathan - Original Message - From: Vitaly V. Chaban vvcha...@gmail.com To: gmx-users gmx-us...@gromacs.org Sent: Sunday, August 23, 2015 10:36:12 AM Subject: Re: [gmx-users] simulations of ice beginning to spin I suggest you to make

Re: [gmx-users] calculate avarage and maximum non-bonded energy between energy groups

1) g_energy 2) g_analyze -f energy.xvg 3) Divide by 3 I do not know the physical sense of the maximum interaction energy. On Mon, Aug 24, 2015 at 4:25 PM, Tushar Ranjan Moharana tusharranjanmohar...@gmail.com wrote: Hi everyone, I want to calculate the average and if possible maximum

Re: [gmx-users] Force field parameterisation

The only thing you need is to transfer partial charges. This can be done using a copy-paste tool. The Amber FF is within gromacs distribution, so the needed bond lengths will be picked up implicitly after you specify bonded atoms, e.g. using x2top or by hand. On Sat, Aug 22, 2015 at 8:28 AM,

Re: [gmx-users] OPLS and GROMOS forcefields

Ionic systems exhibit quite a few differences from molecular liquids. Usage of GROMOS or OPLS force fields will bring significant inaccuracies. Search for the force fields for ionic liquids. E.g. look for numerous developments coming from my group. On Fri, Aug 21, 2015 at 6:08 PM, Stella

Re: [gmx-users] simulations of ice beginning to spin

I suggest you to make a movie... Maybe, indeed, something is wrong with triclinic box definition (?) This not a rotation problem, since your crystal is outside the box at the end. Thus, the box which VMD drew is not the box which gromacs used during dynamics. On Fri, Aug 21, 2015 at 9:13

Re: [gmx-users] binding free energy

needs administrative privileges On Sun, Aug 16, 2015 at 1:41 PM, elham tazikeh elham.tazi...@gmail.com wrote: Dear Users for g_mmpbsa installation (by using source code and APBS 1.4 and gromacs 4.6.7) after below command: pdfco@pdfco-X:~/g_mmpbsa/build$ cmake -DGMX_PATH=/opt/gromacs \

Re: [gmx-users] Pdb file

L_BFGS On Tue, Aug 11, 2015 at 11:37 PM, Sunil Ghimire ghimiresuni...@gmail.com wrote: I created the pdb file by genconf but the system was not minimized, i got positive potential energy. What may be the problem? On 11 Aug 2015 19:38, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, gmx

Re: [gmx-users] Force-field bias???

I believe, yes, it can. Dihedrals can make a big difference... On Wed, Aug 5, 2015 at 7:24 AM, SAPNA BORAH sapnauser...@gmail.com wrote: Dear all, I have a general query about unfolding simulations. Is there a bias among force-fields selected for unfolding, i.e. is it possible that

Re: [gmx-users] Error:EM did not converge while using polarizable ion

The largest force suggests that some atom somehow gets onto another atom. Looking at the topology file is necessary to issue further guesses. I am not sure that Fmax 1 (which units?) is an adequate criterion... On Mon, Aug 3, 2015 at 8:09 PM, Justin Lemkul jalem...@vt.edu wrote: On

Re: [gmx-users] getting .gro file

editconf -f conf.pdb -o conf.gro -box X Y Z On Mon, Aug 3, 2015 at 10:44 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Maybe you don't need one. See http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file Mark On Mon, Aug 3, 2015 at 3:36 PM

Re: [gmx-users] Fwd: DFTB implementation

You need to provide path to the DFTB+ executable and specify the MM part in gromacs. Take care of versions of both codes! On Sat, Aug 1, 2015 at 3:01 AM, Zhenyu Meng fdmm1...@gmail.com wrote: Hi Justin, I read the manual and it mentions how to specify QM/MM parameters, but no detail is