Dear all,
Does anyone know how to obtain speed of sound, c, in a liquid? c is
defined as square root of dP/drho (pressure change with density) at
constant entropy
My idea is to run a series of NPT simulations to obtain density at each P,
to get dP/drho. However, I am not sure how to ensure a
into
the evacuated region.
On Thu, Apr 4, 2013 at 1:20 PM, Elisabeth katesed...@gmail.com wrote:
Dear Dr. Moura,
Thank you for your answer. I equilibrated the cell under NPT and then
extended the Z direction to get a surface. Since I run NVT and Z is
extended, I see no pressure dependence and surface
Hi Vitaly,
To get surface tension one needs to extend Z to get a surface. From bulk it
is not possible to create a surface.
My problem is NVT crashes at step 0 and no energies or any other output
file is written...
On 5 April 2013 10:25, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
Hi all,
On 5 April 2013 16:34, Dr. Vitaly Chaban vvcha...@gmail.com wrote:
But you have conf.gro
On Fri, Apr 5, 2013 at 10:29 PM, Elisabeth katesed...@gmail.com wrote:
Well I am not getting the trajectory. Simulation crashes before any step
is calculated :(
On 5 April 2013 11:20, Dr. Vitaly
into the box and not from an external pressure bath (I would stick to NVT
for such a model). Among the possible issue you might face, the gas would
probably be partially miscible in the liquid phase for high pressures.
I hope it helps.
cheers
Andre
On Wed, Apr 3, 2013 at 11:07 PM, Elisabeth
Hello all,
Does anyone know how one can study the effect of pressure on surface
tension of pure liquids?
Thanks,
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Dear all,
I am trying to get the density profile for my liquid-vacuum interface using
g_density -f trr -s tpr however g_density gives Segmentation fault. Does
anyone had clue what could be wrong? Please comment, Thanks.
Group 0 ( System) has XXX elements
Group 1 (
Hi Justin,
Do I have to read less frames to circumvent the problem? I know g_density
has been used for this purpose so there should be a way to resolve this. I
am reading 1000 frames...
Thanks
On 2 April 2013 12:40, Justin Lemkul jalem...@vt.edu wrote:
On 4/2/13 11:57 AM, Elisabeth wrote
Elisabeth -
The only explanation is that you actually DID NOT extend the box in Z
direction. Look at the last line of confout.gro.
g_density -d Z gives you a [local] density versus Z coordinate.
Dr. Vitaly Chaban
On Mon, Apr 1, 2013 at 5:33 PM, Elisabeth katesed...@gmail.com wrote:
Hi Vitaly
does not read either MDP,
or GRO, or TOP, or anything except CPT.
Dr. Vitaly Chaban
On Mon, Apr 1, 2013 at 7:10 PM, Elisabeth katesed...@gmail.com wrote:
Hi vitaly,
The initial structure is indeed extended but the final output.gro is not.
I think its because I am using the cpt file from
Dear all,
In order to get density profile of a pure system the box has to get
extended in one drection (e.g Z) as we do for surface tension calculations
or density profile
can be also obtained from the usual box filled up with the molecules
without need for empty space in Z
Thanks for any
cells provides the profile I am after. Do you have any clue
whether or not the cell has to be extended in one direction to obtain the
density profile?
Thanks!
On 31 March 2013 12:21, Justin Lemkul jalem...@vt.edu wrote:
On 3/31/13 11:41 AM, Elisabeth wrote:
Dear all,
In order to get
*
*ref_p = 50 ** *
gen_vel = no
gen_temp= 500.0
gen_seed= 173529
constraints = none
constraint-algorithm = lincs
On 31 March 2013 12:47, Justin Lemkul jalem...@vt.edu wrote:
On 3/31/13 12:27 PM, Elisabeth wrote:
Thank
Thanks Vitaly. I am wondering what is the use of semiisotropic with 0
compressibility in Z then? I was hoping to run NPT to secure a fixed
pressure.
I also wanted to know if surface tension can be also calculated under NVT
(if NPT fails for this puporse)
Thanks!
On 31 March 2013 14:01, Dr.
Hi all,
I wanted to use Pcoupltype = semiisotropicbut I am not clear
about the compressibility settings if I want to keep Z directions fixed in
my system and letting X and Y change. Which case 1 or 2 is correct for semi
isotropic option?
1) compressibility = 3.5e-5 3.5e-5 0
2
Hi Justin,
The corect value is 3.5e-5 but I thoiugh x/y means the ratio od these two.
If thats nto the case I guess compressibility = 3.5e-5 0 is the
correct value. What do you think?
On 30 March 2013 11:41, Justin Lemkul jalem...@vt.edu wrote:
On 3/30/13 11:39 AM, Elisabeth wrote:
Hi
Deal all,
I am trying to build up my alkane system to calculate the surface tension a
fixed pressure. Here are the steps:
1- First I did a 10 ns NPT to equilibrate the box and used the last frame
gro and cpt file as input for the next step
2- I extended the box in Z to more than twice the
On 10 February 2012 09:41, Mark Abraham mark.abra...@anu.edu.au wrote:
On 11/02/2012 1:19 AM, Elisabeth wrote:
Hello all,
Does the shift function use group based truncation?
See the discussion of charge groups in manual section 3.4.2.
Thanks Mark.
-1- First of all if I am right
Hello all,
Does the shift function use group based truncation? In the manual I see: by
using shifted forces there is no need for charge groups (=group based?!) in
the neighbor list?
Can anyone shed some light on calculation of shifted forces?
Thanks,
Eli
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Hello all,
Does the shift function use group based truncation?
See the discussion of charge groups in manual section 3.4.2.
Thanks Mark.
-1- First of all if I am right charge groups in gromacs language in
identical to group based truncations?
Manual 342: This reduces the cut-off
Hi all,
Can you please guide me how one can calculate fraction of gauche+ and
gauche- defects in the center of a polymer chain?
Appreciate you help.
Juliete
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Dear experts,
I am working on a pure polymer melt system under NPT and at a given T,
pressure is increased up to around 1000 bar. However, the phase diagram of
the polymer is indicating that at this T, as pressure is increased to above
500 bar, system falls below the melting point.
I mean I am
Hello,
I am trying to figure out how to plot or obtain the average values of
Gyration radius from different subgroups of index file. index file prompts
for a single group and I need to calculate the averages for all subgroup by
hand.
Is there any way to compute averages or plot all subgroups
On 20 August 2011 21:20, Mark Abraham mark.abra...@anu.edu.au wrote:
On 20/08/2011 8:02 AM, Elisabeth wrote:
Dear experts,
I am intending to calculate the equilibrium density of a pure hydrocarbon
at different pressures , at 425 K. The normal boiling point of the liquid is
around 350 K
Dear experts,
I am intending to calculate the equilibrium density of a pure hydrocarbon at
different pressures , at 425 K. The normal boiling point of the liquid is
around 350 K. For pressures below 100 bar densities I am getting from NPT is
in accurate. I start form a structure which is
getting from my runs are unreliable?
Appreciate any clarification.
Thank you,
Best,
On 15 August 2011 19:34, Mark Abraham mark.abra...@anu.edu.au wrote:
On 16/08/2011 7:05 AM, Elisabeth wrote:
Dear all,
I noticed that applying Parrinello-Rahman (PR) pressure coupling even after
apply
berendsen barostat combined with v-rescale thermostat to equilibrate or
since I am using berendsen barostat, T coupling scheme has to be also
berendsen?
Thanks,
On 16 August 2011 13:17, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:f
Hello,
Thank you. I am looking
Dear all,
I noticed that applying Parrinello-Rahman (PR) pressure coupling even after
equilibration with berendsen does not lead to target value for pressure when
;Bonds
constraints = none
is used. I tried Berendsen for to get fixed pressure ( 50 bar) but in the
next run PR
On 3 August 2011 15:31, Dr. Vitaly V. Chaban vvcha...@gmail.com wrote:
On Wed, Aug 3, 2011 at 3:17 PM, Elisabeth katesed...@gmail.com wrote:
On 2 August 2011 15:29, Dr. Vitaly V. Chaban vvcha...@gmail.com wrote:
Hello,
I wanted to know your ideas on calculation of heat
Hello,
I wanted to know your ideas on calculation of heat of vaporization using a
single phase run rather than running two separate simulations for liquid and
gas!
1- Two separate simulations for liquid and gas
DHvap = Ugas - Uliq + RT
1a: total liquid potential - *total* potential of a single
:
Elisabeth wrote:
Thanks Justin for your guidance. By following your tips, I have now all
the parameters I need... Please let me know if I am missing any [ angletypes
] or [ dihedraltypes ] for a hydrocarbon molecule.
Seems fine to me; grompp will complain if something is missing
Hello all,
Can anyone tell me how gromacs may be cited besides
Principal Papers
1. Berendsen, et al. (1995) *Comp. Phys. Comm.* *91: *43-56.
(DOIhttp://dx.doi.org/doi:10.1016/0010-4655%2895%2900042-E_,
Citations of this
paperhttp://scholar.google.com/scholar?cites=6703762643559347673hl=en
Hello to all,
I am looking for bonded and nonbonded parameters for C H atoms in saturated
hydrocarbons.
atom types are:
Carbon atoms opls_135 opls_136
H opls_140
opls_135 12.01100 ; alkane CH3
opls_136 12.01100 ; alkane CH2
opls_1401.00800 ; alkane H.
Please help me out
On 3 June 2011 03:25, Mark Abraham mark.abra...@anu.edu.au wrote:
On 3/06/2011 3:06 AM, Elisabeth wrote:
Hello all,
I am getting the error below at the very beginning of the simulation (both
serial and parallel). I am sure I did not encounter this problem before with
the same input files
Hello all,
I am getting the error below at the very beginning of the simulation (both
serial and parallel). I am sure I did not encounter this problem before with
the same input files. This has just happened now. I really have no clue why
this is happening. could you please help me? Thank you all
Hello Justin,
Thank you. I am using
gmxdump -s *.tpr -om to produce mdout.mdp file but I dont see box vector
information. This error happens at the very beginning. I see no steps are
calculated.
On 2 June 2011 13:11, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
Hello all
have been using the same gro file before and never got such error). Do you
recommend I reinstall 4.5.4 ?
Appreciate any help...
Regards,
On 2 June 2011 14:47, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
Hello Justin,
Thank you. I am using
gmxdump -s *.tpr -om to produce
Dear all,
I am trying to study the effect of pressure on total potential of my system
(8 polymer chains). My problem is that I dont see a systematic effect of
pressure on potentials and I cant judge if different pressures increase or
decrease potential. This is the critical observable in my
Dear experts,
I have been considering effect of fixing bond lengths in my system
(constraints= none / all-bonds) on equilibrated density using NPT runs with
4.5.4. I am showing two set of results for two ref pressures of 10 and 70
bar. in case of constraints= none I had to employ a 0.5 fs
On 20 May 2011 23:04, Mark Abraham mark.abra...@anu.edu.au wrote:
On 21/05/2011 10:45 AM, Elisabeth wrote:
Dear experts,
I have a box of pure hexane with density of around 50 SI (size 7nm). With
the settings below I get error:
vol 0.65 imb F 3% step 42100, will finish Fri May 20 18:54
On 21 May 2011 19:02, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
On 20 May 2011 23:04, Mark Abraham mark.abra...@anu.edu.au mailto:
mark.abra...@anu.edu.au wrote:
On 21/05/2011 10:45 AM, Elisabeth wrote:
Dear experts,
I have a box of pure hexane
Dear experts,
I have a box of pure hexane with density of around 50 SI (size 7nm). With
the settings below I get error:
vol 0.65 imb F 3% step 42100, will finish Fri May 20 18:54:05 2011
Warning: 1-4 interaction between 1246 and 1249 at distance 3.580 which is
larger than the 1-4 table size
Hello,
Can anyone suggest some tutorials or sample top files for simulations
involving freezing of groups? I dont see much info in chapter 5 of manual.
Thanks,
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?
Please guide me, I am stuck on this..
Thanks,
On 9 April 2011 20:56, Mark Abraham mark.abra...@anu.edu.au wrote:
On 8/04/2011 12:18 PM, Elisabeth wrote:
Hello everyone,
I have encountered a simple problem. For a homogenous system what
g_energy reports is dependent on the system size
case using -nmol gives per mol energies and somehow
predict AB from them? Does this make sense?
Please guide me, I am stuck on this..
Thanks,
On 9 April 2011 20:56, Mark Abraham mark.abra...@anu.edu.au wrote:
On 8/04/2011 12:18 PM, Elisabeth wrote:
Hello everyone,
I have encountered a simple
Hello everyone,
I have encountered a simple problem. For a homogenous system what g_energy
reports is dependent on the system size and one needs to use -nmol option to
divide energies by number of molecules to obtain per mol values.
I am attempting to extract interaction energies between species
Hello Justin,
Several days ago you answered my question about calculating nonbonded terms:
Question: If I want to look at nonboded interactions only, do I have to add
Coul. recip. to [ LJ (SR) + Coulomb (SR) ] ?
Answer: The PME-related terms contain both solute-solvent, solvent-solvent,
and
On 6 April 2011 15:01, Michael Brunsteiner mbx0...@yahoo.com wrote:
Elisabeth,
You CAN, in fact calculate the contribution of the reciprocal part
of the PME energy to the binding energy between two components in
a heterogeneous system, its just quite tedious...
say, your system
On 6 April 2011 19:28, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
On 6 April 2011 15:01, Michael Brunsteiner mbx0...@yahoo.com mailto:
mbx0...@yahoo.com wrote:
Elisabeth,
You CAN, in fact calculate the contribution of the reciprocal part
of the PME energy
Elisabeth wrote:
Dear David,
I followed your instructions and calculated Heat of vaporization of my
alkane once with one molecule in gas phase (no cutoff) and once with
equivalent number of molecules as in liquid phase as Justin suggested.
Results are as follows:
To get heat
Dear David,
I followed your instructions and calculated Heat of vaporization of my
alkane once with one molecule in gas phase (no cutoff) and once with
equivalent number of molecules as in liquid phase as Justin suggested.
Results are as follows:
*one single molecule in gas phase*
Energy
in your mail:
On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
Dear all,
I intend to obtain vaporization heat per volume for a /pure alkane
system/. Here is the steps I am taking. Please correct me.
1- Obtain total energy of system (kinetic+potential
On 31 March 2011 12:58, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
in your mail:
On 30 March 2011 15:30, Justin A. Lemkul jalem...@vt.edu mailto:
jalem...@vt.edu wrote:
Elisabeth wrote:
Dear all,
I intend to obtain vaporization heat per volume
Dear gromacs users,
I am planning to produce C-C rdf for my system and I have difficulty making
the index file with a group of all C in the system, [Carbon] . .If there are
thousands of atoms in the system do I have to go through the top file and
note down C atom numbers and use those numbers to
Dear all,
I asked this question a few days ago but did not receive a solid answer. Has
anyone tried to produce the properties below? Can you comment on accuracy of
these properties using g_energy?
Thermal expansion coeff. (NPT): Enthalpy, Vol, Temp
Isothermal compressibility:
Dear all,
I intend to obtain vaporization heat per volume for a *pure alkane system*.
Here is the steps I am taking. Please correct me.
1- Obtain total energy of system (kinetic+potential) and divide by number of
molecules to obtain energy per mol of molecules. g_energy -f *.edr -nmol XXX
2-
Thanks David for replying me. I appreciate your attention to comment on
the following short inquiries.
1- g_energy says:
you will need to give the number of constraints per molecule –nconstr and
for water this is 3. Can you elaborate on how to set this option. When
constraints=
Dear all,
I am trying to calculate Cv of a pure alkane 125 molecules with actual
density, and here is what I have done:
1-
Cv: Run NVT g_energyselect T and Etot=total energy
As I issue g_energy *.edr
Heat Capacity Cv: 12.4787 J/mol K (factor = 0.000369503)
And when I choose –nmol
Dear all,
I performed surface tension calculations vs. different system size (NVT, mdp
file is included at the end). The reported surface tension for hydrocarbon I
am studying is 18 mN/m at 20C. I am getting ~ 175 bar nm from g_energy which
means surface tension of around 9 mN/m. For box size 3
Thanks for your help. :)
On 23 March 2011 07:47, Justin A. Lemkul jalem...@vt.edu wrote:
Mark Abraham wrote:
On 23/03/2011 3:39 PM, Elisabeth wrote:
Thanks Mark for the hints. I am using a pre equilibrated box for both
runs. Can you again explain how Can I interpret this from
On 22 March 2011 22:31, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
Hello,
I did two simulations on the same system using versions 4.0.7 and 4.5.3.
It seems like the unit of surface tension is not the same in these versions
because I am getting ~250 KJ/mol an in 4.0.7
On 22 March 2011 22:46, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
On 22 March 2011 22:31, Justin A. Lemkul jalem...@vt.edu mailto:
jalem...@vt.edu wrote:
Elisabeth wrote:
Hello,
I did two simulations on the same system using versions 4.0.7
, Mark Abraham mark.abra...@anu.edu.au wrote:
On 23/03/11, *Elisabeth * katesed...@gmail.com wrote:
On 22 March 2011 22:46, Justin A. Lemkul jalem...@vt.edu wrote:
Elisabeth wrote:
On 22 March 2011 22:31, Justin A. Lemkul jalem...@vt.edu mailto:
jalem...@vt.edu wrote:
Elisabeth
- my last question is how can I make sure surface tension reported by
g_energy is the equilibrated one. RMSD is very big compared to surf. ten. !
Thanks for your time.
Elisabeth
**
if you are interested in the surface tension of a pure liquid, which I
dimension? then how much increase in one direction is
reasonable? (If I have a 2 nm box).
Also Can you please introduce some text book?
Thank you,
Best regards,
2011/3/15 André Farias de Moura mo...@ufscar.br
Dear Elisabeth,
actually, it is the other way around, you need increase the box length
Dear gmx users,
Since I am new to surface tension topic I need to ask very trivial
questions. Please help me out with these simple questions.
As a starting point I am going to calculate surface tension of a pure alkane
in a cubic box and compare with experimental values.
1- g_energy is giving
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