On 2011-03-11 08.58, Thomas Koller wrote:
Hello,
i) I use a NPT ensemble to get the heat capacity c(p). But I always get c(V)
when I use option -vis where some properties are listed. What is the standard
way to extract the isobaric heat capacity? Which tool should I use?
ii) The thermal compr
Dear all,
a very quick question: I would like to know if a checkpoint file produced
with a simulation with Gromacs contains really ALL information needed to
restart a simulation; or better, if I keep only the .cpt file and the .xtc
file of a simulation, which information I lost (apart from the prec
On 11/03/11, Anna Marabotti wrote:
>
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> Dear
> all,
>
> a very quick
> question: I
> would like to know if a checkpoint file produced with a simulation with
> Gromacs
> contains really ALL information needed to restart a simulation; or better, if
> I
> keep only th
Iam working with a NMR protein containing Zn ions. After generating topology
file using pdb2gmx, it is generating topology files containing Protein and
ions separately. How can i solve this.
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Plea
After I type :"mdrun -s pr.tpr -o pr.trr -c b4md.gro -g pr.log -e pr.edr &
",then there are a error:Fatal error: ci = -1 should be in 0 .. -1 [FILE
nsgrid.c, LINE 210] I do not know what is " ci " meaning for and where is
the problem? thank you !
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gmx-users mailing listgmx-users@grom
You mean that I take the fluctuations of enthalpy (= total energy and PV) and
fluctuations of temperature and make simply the ratio to get c(P)?
Thomas
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Rausch, Felix wrote:
Dear Gromacs users,
I would like so simulate a protein with phosphorylated amino acids with
Gromacs 4.5.3. To do so, I got the "ffG43a1p" forcefield available from
the user contributions section (subsection force fields) and adapted the
parameters given there to Gromo
chitrala kumaraswamynaidu wrote:
Iam working with a NMR protein containing Zn ions. After generating
topology file using pdb2gmx, it is generating topology files containing
Protein and ions separately. How can i solve this.
pdb2gmx -chainsep (-merge in old versions).
-Justin
--
=
zen...@graduate.org wrote:
After I type :"mdrun -s pr.tpr -o pr.trr -c b4md.gro -g pr.log -e pr.edr
& ",then there are a error:Fatal error: ci = -1 should be in 0 .. -1
[FILE nsgrid.c, LINE 210] I do not know what is " ci " meaning for
and where is the problem? thank you !
http://www
On 2011-03-11 12.05, Thomas Koller wrote:
You mean that I take the fluctuations of enthalpy (= total energy and PV) and
fluctuations of temperature and make simply the ratio to get c(P)?
Thomas
Did you try what I suggested? g_energy prints all the properties you
requested. You need gmx 4.5 to
Hi,
I am doing MD simulation of protein-ligand system using G53a6 as
forcefield. I got the ligand.itp file for ffG53a6 from the ATB
(Automated Topology Builder) server. I included the ligand.itp in the
.top file, generated an octahedron solvation box, solvated it and did
the grompp step before
Dear Justin,
I checked my working directory (including ff-directory) again and found some
entries (i added myself) with the old uppercase spelling in the nonbonded.itp.
After editing these lines everything works well. Conclusion: I have to learn
using the command grep properly :)
Thank you v
Meenakshi wrote:
Hi,
I am doing MD simulation of protein-ligand system using G53a6 as
forcefield. I got the ligand.itp file for ffG53a6 from the ATB
(Automated Topology Builder) server. I included the ligand.itp in the
.top file, generated an octahedron solvation box, solvated it and did
th
Dear all,
I have got a question about the PMF profile determined with umbrella sampling
calculation.
If z is the reaction coordinate, is it possible to calculate a PMF profile
with umbrella sampling if we have a repulsive force at 0http://lists.gromacs.org/mailman/listinfo/gmx-users
Please searc
Dear experts,
I have been trying to do NVT on a system (a single polyethylene chain in 110
hexane) in the past few days but still no success. For some reason
simulations are taking much longer than before. A run that used to complete
in a few hours is taking several weeks. I am wondering if there
Hi,
While running a simulation of capped alanine in an implicit solvent the
molecule appears to collapse on itself such that the atoms have coordinates
of 0,0,0 or some even have NaN. Has anyone else had this problem or any
suggestions?
The simulation was run using GROMACS 4.5 with the amber96ff w
Andrew Mauro wrote:
Hi,
While running a simulation of capped alanine in an implicit solvent the
molecule appears to collapse on itself such that the atoms have
coordinates of 0,0,0 or some even have NaN. Has anyone else had this
problem or any suggestions?
Sounds like http://www.gromacs.o
I have version 4.0.5 and there is no enthalpy in the g_energy tool. Do you see
a chance to calculate the isobaric heat capacity as well as the thermal
compressibility, which is also not shown?
Thomas
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Schon gehört? GMX hat einen genialen Phishing-Filter in die
Toolbar eingebaut! http://www.gm
On 2011-03-11 19.53, Thomas Koller wrote:
I have version 4.0.5 and there is no enthalpy in the g_energy tool. Do you see
a chance to calculate the isobaric heat capacity as well as the thermal
compressibility, which is also not shown?
Thomas
Then you have to compute the enthalpy yourself by su
> I am doing free energy calculation in Gromacs and want to get an error
> estimate of my results. Is it possible to compute the autocorrelation time
> of dVpot/dlambda in Gromacs using a certain length of trajectory such as 10
> ns? Thanks a lot
The amount of simulation time required to compute t
Hi Michael:
Thanks for the reply! I did the following command: g_analyze -f
energy.xvg -ac out.xvg
and in out.xvg I saw the following lines, it seems like a autocorrelation
decrease over time. Does that mean the autocorrelation time here is
infinite? Thanks
Steve
# This file was cre
I am running MD simulations on Liquid/Liquid interfaces and measuring the
interfacial tension between them. I have found that the readings in NVT
simulations are close to experimental values, but have a lot of variation.
I run NPT simulations on the exact same system and find the results show
very
Thanks,
the equation for the heat capacity is:
c(P) = delta(H(average))/delta(T(average))
So do it have to take the fluctuations (which are listed with g_energy) of
U(tot) and pV as well as of T to calculate c(P)? The problem is the delta.
The same is with the thermal compressibility:
a(P) =
Dear gmxers,
I want to perform a constant-NPT MD simulation using gmx. By default, a,b,c
of 3D pbc box can change to compatile with the density. Whether can gmx change
a,b of 3D pbc box but unchange c? Please give me some hints. Thanks a lot.
Yours sincerely,
Chaofu Wu, Dr.--
gmx-users
Dear All
How can I read and work on outputs of one version of Gromacs with tools of
other version?
Because I have run my program on cluster(version 4.5.3) ,but I need to work
with them in v.4.0.7
Suppose I have to work with this version and there is not any way to change
versions neighter on clu
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