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
On Sun, Mar 13, 2016 at 7:18 PM, VITALY V. CHABAN
> wrote:
>
>> Upon free energy calculations via continuous decoupling,
>>
>> free-energy = yes
>> couple-moltype = MOL
>> couple-lambda0 = vdw-q
>> couple-lambda1 =
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
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, M
016-01-26 13:14 GMT+01:00 Mark Abraham :
> >
> > > Hi,
> > >
> > > There's no need to modify the code to do this. You can schedule your
> own
> > > halt e.g. 10ns from the end by choosing nsteps, save that checkpoint
> > file,
> > > and
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 time points (e.g. 10ns
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 conditions
> (conforma
What are the units of surface tension derived thru g_energy?
I am confused with the header: (kJ mol\S-1\N)
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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 mo
it is short, but this is not the reason for crash.
this sort of problems come from topology.
On Sat, Jan 16, 2016 at 6:15 AM, Marco Franzoi
wrote:
> Thanks vitaly. Can it be that the nvt equilibration is too short for such
> a huge system?
> Il 16/gen/2016 03:42, "VITALY
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, I run an em, a 0.1 ns nvt a
or 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
> wrote:
>
>> The force constants wer
ath
>
>
>
> On Thu, Jan 14, 2016 at 6:53 PM, VITALY V. CHABAN
> wrote:
>
>> 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 f
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 obtained the same results when
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
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 major difference
> betwen addin
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,
>
> shanu
>
> On Tue, Jan 12,
What is the charge of your infinite periodic system if your unit cell
charge is 5e?
On Tue, Jan 12, 2016 at 11:54 AM, sun wrote:
> Hello Everyone
> I want to know how to change the non-integral charges? I am simulating a
> pentameric model of protein in water and the net charge comes out to b
ok
thank you
On Wed, Dec 16, 2015 at 11:33 AM, Justin Lemkul 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 bond length (as in ITP)?
&
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.
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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
angstrom.
>
> Thanks for your kind reply.
>
> Sudip
>
> On Mon, Dec 7, 2015 at 10:17 PM, Vitaly V. Chaban
> wrote:
>
>> Mine converges.
>>
>> What about box size?
>>
>>
>>
>>
>>
>> On Fri, Dec 4, 2015 at 7:14 AM, Sudip Das wr
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 exactly, rather it converges t
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,
>
>
>
> I generated the initial str
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 an "infinite" filament
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 for your molecule.
> There ar
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 :
>
> > I compute the energy ACF by using
> >
> > g_energy_
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.
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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 list Gromacs
>
>
> Dear Gromacs user,
>
> I did
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 default, GROMACS use
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 s
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 which the parameters are used
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
no
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 frame
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
w
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 (e.g. DLVO) and implicit
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 simulated a simple prot
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 needed to know.
>
> Victor
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 consider the flat-bottomed
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 the water from the a
See [nonbond_params] topology section, I guess...
On Sun, Sep 27, 2015 at 6:18 PM, maryam haji wrote:
> Dear Users,
>
> I want to simulate CNT in water solvent with CHARMM27 force field. The used
> parameters for simulation of CNT follows:
>
>
>
> The .n2t file is:
>
>
>
> CCA0.00
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
> contains 8mers and monomers of cel
Thermodynamic equilibrium is concluded from the evolution of thermodynamic
quantities, not presence or absence of "blocks within the box".
On Sat, Sep 19, 2015 at 11:19 AM, Justin Lemkul wrote:
>
>
> On 9/19/15 10:07 AM, Pallavi Banerjee wrote:
>
>> Hello Users,
>>
>> I have a system of th
See the reactive force fields or cheap electronic-structure-based MD.
You will not be able to reproduce CO2+H2O<->H2CO3 in GROMACS.
On Sun, Sep 13, 2015 at 1:55 PM, hzj1000 wrote:
> So how to deal with CO2 ~H2O interaction in GROMACS?
>
> 发自我的小米手机
> 在 2015年9月14日 上午12:38
CO2/H2O bonding is irreproducible using LJ only.
On Sun, Sep 13, 2015 at 12:36 PM, Justin Lemkul wrote:
>
>
> On 9/13/15 11:26 AM, Zhongjin He wrote:
>
>> Dera GMX user,
>>
>>
>> I have simulated CO2 in water, using SPC/E for water, EPM2 model for CO2.
>> I decide to use Lorentz-Berthelot mix
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 archive at
> http://www.gromacs.o
g tau_t = -1). What
> would be reasons?
>
> ------
> *From: *"Vitaly V. Chaban"
> *To: *"gmx-users"
> *Sent: *Thursday, September 10, 2015 8:37:52 PM
> *Subject: *Re: [gmx-users] NVE+NVE: Two groups: one with Tcouple while
> the
Sure.
N2 heats the large moleculle which dissipates heat much more slowly and
does not have a thermostat to help it.
On Thu, Sep 10, 2015 at 9:09 PM, Guiyuan Mo wrote:
> Hi,
>
>
> I am modelling a box with two groups of molecule: N2 and C12H26.
> 1. Initially, NVT was used for both:
>
> ; Te
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: /root/workdir_kn/gromacs-
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 see weather I
> assign
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, n
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, S
y of pure iso propanol and used the closest definition
> to the real value. Iso propanol is used as co-solvent with water with a
> water:iso propanol ration of 90:10. I will just use my derived parameters
> then.
>
> Thanks for your replies.
>
> Max
>
>> On Sep 2, 20
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 5.1. [plot of energy at
> h
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:
> Hi
> No, I don't have a cpt
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 s
Try 5-20fs.
On Wed, Sep 2, 2015 at 12:06 AM, Aishwary Shivgan
wrote:
> Currently I saving the energies after every 50 fs. Should I decrease more?
> On Sep 2, 2015 3:23 AM, "Vitaly V. Chaban" wrote:
>
>> Sure, viscosity is overestimated, since you do not sa
_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
> wrote:
>>
>> g_energy -vis
>> g_analyze -f visco.xvg
>>
>>
>> The method is handy only for system
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 , however the last
> surface
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 trying to neutralized the pr
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
wrote:
> Hi everyone,
> I want to calculate the average and if possible maximum non-bonded energy
> between d
, but do I need anything in my input file?
>
> Thanks,
> Nathan
>
> - Original Message -
> From: "Vitaly V. Chaban"
> To: "gmx-users"
> Sent: Sunday, August 23, 2015 10:36:12 AM
> Subject: Re: [gmx-users] simulations of ice beginning to spin
>
&
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, N
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 PM,
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 Nick
" needs administrative privileges"
On Sun, Aug 16, 2015 at 1:41 PM, elham tazikeh 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 \
>> -DAPBS14=on \
>>
L_BFGS
On Tue, Aug 11, 2015 at 11:37 PM, Sunil Ghimire
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" wrote:
>
>> Hi,
>>
>> gmx genconf on a small box with a single
I believe, yes, it can. Dihedrals can make a big difference...
On Wed, Aug 5, 2015 at 7:24 AM, SAPNA BORAH 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 unfolding of
> the protein
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 wrote:
>
>
> On 8/3/15 6:38 PM,
editconf -f conf.pdb -o conf.gro -box X Y Z
On Mon, Aug 3, 2015 at 10:44 AM, Mark Abraham 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 Mehrnoosh Hazrat
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 wrote:
> Hi Justin,
> I read the manual and it mentions how to specify QM/MM parameters, but no
> detail is provided. Also it sa
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