Hi,
I have applied distance restraints on my system during MD simulation through
following options:
"disre = simple" and disre_fc = 2000 in .mdp file.
Now i wish to see the energy term corresponding to these restraints in
principle to be written in .edr file. But g_energy programme does not list
I had also had trouble installing gmx (paralley). But now, its solved.
I would suggest you to see that the mpi is running or not.
Here is a sample mpi C program:
#include
#include "mpi.h"
int main( argc, argv )
int argc;
char **argv;
{
int
On 02/06/10, zuole wrote:
Hello,
I've been reading all of the archived questions on the analysis of REMD in Gromacs, and I'm still a bit confused. It appears that the first step is to use the demux.pl script to demultiplex the REMD trajectories. That depends on the kind of analysis you wish
zuole wrote:
Hello,
I've been reading all of the archived questions on the analysis of REMD
in Gromacs, and I'm still a bit confused. It appears that the first step
is to use the demux.pl script to demultiplex the REMD trajectories.
However, I am unable to find this demux.pl file in
the s
Hello,
I've been reading all of the archived questions on the analysis of REMD in
Gromacs, and I'm still a bit confused. It appears that the first step is to use
the demux.pl script to demultiplex the REMD trajectories. However, I am unable
to find this demux.pl file in the src/contrib/scri
to create itp file with OPLS force feild, you can try use GAMESS.
-fairuz-
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On Fri, 2010-02-05 at 15:29 -0500, Matthew L. Danielson wrote:
> Compiling fftw and openmpi seems to finish successfully. The serial
> version of gromacs installed correctly, just when i issue --enable-mpi i
> am seeing this error message (i can attached the config.log if it would
> help):
> "c
On Fri, February 5, 2010 at 1:06:34 PM, Antoine Delmotte
wrote:
> I would like to simulate the CDK9 protein (3BLH in PDB), but there is
one residue (TPO,
> phosphothreonine), which Gromacs does not recognise.
>
> I
found the PRODRG website as well as force field parameters for TPO for
the Gromo
Gard Nelson wrote:
Hi all,
I'm trying to simulate a solvated membrane using Berger's lipids. When
I run grompp, i get the following error:
checking input for internal consistency...
processing topology...
Opening library file ...lipid.itp
Opening library file ...nb_lipid.itp
Opening library
Hi all,
I'm trying to simulate a solvated membrane using Berger's lipids. When I
run grompp, i get the following error:
checking input for internal consistency...
processing topology...
Opening library file ...lipid.itp
Opening library file ...nb_lipid.itp
Opening library file ...bon_lipid.itp
Op
Vitaly V. Chaban wrote:
Yes, I provided all the possible entries in the N2T.although the
problem is the same. I also recreated PDB and re-measured the
distances but everything seems pretty correct in my PDB.
N N 2 S 0.17 S 0.17
F F 1 C 0.14
S S 4 O 0.17 O 0.17 C 0.18
Yes, I provided all the possible entries in the N2T.although the
problem is the same. I also recreated PDB and re-measured the
distances but everything seems pretty correct in my PDB.
N N 2 S 0.17 S 0.17
F F 1 C 0.14
S S 4 O 0.17 O 0.17 C 0.18 N 0.17
C C 4 F 0.
Users,
I am having a problem installing version 4.0.7, specifically the
parallel version. Searching the mailing archives i came across several
posts related to my problem but none seemed to offered a solution to the
error message i am seeing (tried all suggestions). I have root access
to my
Vitaly V. Chaban wrote:
On Fri, Feb 5, 2010 at 9:13 PM, Justin A. Lemkul wrote:
Vitaly V. Chaban wrote:
In this context, it is interesting how X2TOP decides that two atoms
are connected? Only on the base of N2T: if the atom should have 4
neighbours, it looks for the appropriate number of th
On Fri, Feb 5, 2010 at 9:13 PM, Justin A. Lemkul wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> In this context, it is interesting how X2TOP decides that two atoms
>> are connected? Only on the base of N2T: if the atom should have 4
>> neighbours, it looks for the appropriate number of them?
>>
>
> Th
From the Carlson et al. paper where these ATP parameters were published and
through choosing the appropriate amber_X atom types from the .atp (and the
corresponding values for these types in the nb and bon .itp files). As I
mentioned previously you need to add a new O3 atom type to these files
Vitaly V. Chaban wrote:
In this context, it is interesting how X2TOP decides that two atoms
are connected? Only on the base of N2T: if the atom should have 4
neighbours, it looks for the appropriate number of them?
That's correct.
In my case, maybe it considers that 0.18 nm is too much for
Lum Nforbi wrote:
Dear all,
Please, could someone tell me what could be the problem with the
attached LJ plot?
Could it be due to wrong assignment of periodic boundary conditions?
First, do not attach files without file extensions. For those of us who are
security-conscious (some say
In this context, it is interesting how X2TOP decides that two atoms
are connected? Only on the base of N2T: if the atom should have 4
neighbours, it looks for the appropriate number of them?
In my case, maybe it considers that 0.18 nm is too much for two atoms
to be connected?
-- Forward
Dear all,
Please, could someone tell me what could be the problem with the attached
LJ plot?
Could it be due to wrong assignment of periodic boundary conditions?
Thank you,
Lum
RDF_oxyxoy
Description: Binary data
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Hi Thomas !
Creating a new entry in the .rtp, nb.itp needs charge, radius, epsilon
values etc. values. Where to get these values
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Feb 5, 2010 at 6:54 PM, Thomas Piggot wrote:
> Not sure about amb2gmx.pl or acpypi but you can do this by
Antoine Delmotte wrote:
Dear gmx-users,
I would like to simulate the CDK9 protein (3BLH in PDB), but there is
one residue (TPO, phosphothreonine), which Gromacs does not recognise.
I found the PRODRG website as well as force field parameters for TPO for
the Gromos96.1 force field. However,
Dear gmx-users,
I would like to simulate the CDK9 protein (3BLH in PDB), but there is one
residue (TPO, phosphothreonine), which Gromacs does not recognise.
I found the PRODRG website as well as force field parameters for TPO for the
Gromos96.1 force field. However, I would like to use the OPL
Yes. This worked even with my N2T. I will probably recreate my PDB...
On Fri, Feb 5, 2010 at 7:51 PM, Justin A. Lemkul wrote:
>
>
> Vitaly V. Chaban wrote:
>>
>> Justin,
>>
>> Am I correct that X2TOP uses only N2T file to make a topology?
>>
>
> Yes.
>
>> I made the full line for Sulphur but it
Vitaly V. Chaban wrote:
Justin,
Am I correct that X2TOP uses only N2T file to make a topology?
Yes.
I made the full line for Sulphur but it didn't change the situation.
It looks strange that X2TOP notices 3 bonds although I propose to have
4 bonds (and they are present). If I propose 3 bo
Justin,
Am I correct that X2TOP uses only N2T file to make a topology?
I made the full line for Sulphur but it didn't change the situation.
It looks strange that X2TOP notices 3 bonds although I propose to have
4 bonds (and they are present). If I propose 3 bonds, it readily gives
an output... Th
[Alexey Shvetsov, 18.12.2009]:
>On Пятница 18 декабря 2009 23:47:34 David van der Spoel wrote:
>>Alexey Shvetsov wrote:
>>>On Пятница 18 декабря 2009 19:29:15 XAvier Periole wrote:
Dears,
we have been trying to run gmx-4.0.X on new machines with the
Intel I7 CPUs. It is a quad core
Vitaly V. Chaban wrote:
Hi,
This can be the reason when X2TOP gives the following error:
"
Fatal error:
No forcefield type for atom S (2) with 3 bonds
"
?
I try to translate PDB of the TFSA anion
OO
|| ||
F3C-S-N-S-CF3
|| ||
OO
into topology.
My
Hi,
This can be the reason when X2TOP gives the following error:
"
Fatal error:
No forcefield type for atom S (2) with 3 bonds
"
?
I try to translate PDB of the TFSA anion
OO
|| ||
F3C-S-N-S-CF3
|| ||
OO
into topology.
My PDB contains optimized geome
OK. I found my function type "1" and used k_b in [kJ/mol/nm^2].
Vitaly
On Fri, Feb 5, 2010 at 5:39 PM, Erik Marklund wrote:
> It depends on the function type. See the table "Intramolecular interaction
> definitions" in chapter 5 of the gromacs manual. There you can se the units
> associated wit
It depends on the function type. See the table "Intramolecular
interaction definitions" in chapter 5 of the gromacs manual. There you
can se the units associated with the different kinds of interactions.
Erik
Vitaly V. Chaban skrev:
Hi,
In what units does gromacs MD engine treats harmonic bo
Hi,
In what units does gromacs MD engine treats harmonic bond constants?
In the tutorial, there is a hint about fourth-power potential (related
to GROMOS-96 FF) which I guess should have a constant in
[kJ/mol/nm^4], but not in [kJ/mol/nm^2]. Although it seems by the
absolute value that in the exis
Not sure about amb2gmx.pl or acpypi but you can do this by hand. Consult
the GROMACS manual (Chapter 4) for the equations to convert the
parameters into GROMACS format.
I would also say that the easiest way would be to create a new entry in
the .rtp and then also add the appropriate bonded par
Hi Par,
Thank you so much for your explanations, it is very helpful.
Stéphane
Hi Stephane,
> I am doing some tests with the CHARMM port in GROMACS. Before to start
> more extensive simulations with this ff
> I have performed a short run of 1000 TIP3-CHARMM water molecules in a
> cubic duri
Hi Stephane,
> I am doing some tests with the CHARMM port in GROMACS. Before to start
> more extensive simulations with this ff
> I have performed a short run of 1000 TIP3-CHARMM water molecules in a
> cubic during at T=300 K and P=1.015 bar with v-rescale and PR as
> thermostat and barostat. I
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