Mark, thanks for explanation.
So if I understood that graph correctly I must define R1=1 and R2=2 values
from my example 1Rij2 to obtain quadratic restrain forces done in my
distance range ( from 1 to 2 angstr). In other words this would restrains
the i and j atom to the desired distance by the
Hi.
I'm testing a forcefield with a combination of CPT and NVT MD
simulations of a polymer in water. I adopted the equilibration steps
form the CHARMM equilibration steps:
1. Fix solute (using define = -DPOSRES ).
a) 10.000 steps of steepest descent minimization
b) 10.000 steps of conjugated
It's appeared two new questions on the same topic :)
1) By the way, new error have been occured when I've tried to use
multi-core station with MPI to calculate such restrained model ( I have no
same problems on the single station )
the error
Fatal error:
Time or ensemble averaged or multiple
Hi Gromacs Specialist,
1. I need the help regarding the PCA
(Principle component analysis ).
If anyone can suggest me a good review
article and some tips how to analyse PCA result
I am very new to simulation study.
I read GROMACS manual, but I need
any review type article.
Dear Gromacs Users,
I am running mdrun on single node with 8 CPU and getting following error
Fatal error:-
D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are connected
via constraints from the neighbouring cells.
This probably means your constraint length are too long compared
On 14/03/2012 5:50 PM, James Starlight wrote:
Mark, thanks for explanation.
So if I understood that graph correctly
You haven't. The potential is zero between r_0 and r_1. Both the
equation and graph make this clear. The potential is non-zero outside
this range. The force is the negative of
On 14/03/2012 8:39 PM, James Starlight wrote:
It's appeared two new questions on the same topic :)
1) By the way, new error have been occured when I've tried to use
multi-core station with MPI to calculate such restrained model ( I
have no same problems on the single station )
the error
On 14/03/2012 5:59 PM, Jernej Zidar wrote:
Hi.
I'm testing a forcefield with a combination of CPT and NVT MD
simulations of a polymer in water. I adopted the equilibration steps
form the CHARMM equilibration steps:
1. Fix solute (using define = -DPOSRES ).
a) 10.000 steps of steepest descent
On 14/03/2012 9:54 PM, PAVAN PAYGHAN wrote:
Dear Gromacs Users,
I am running mdrun on single node with 8 CPU and getting following error
Fatal error:-
D D cell 1 0 0 could only obtain 1520 of the 1521 atoms that are
connected via constraints from the neighbouring cells.
This probably
Dear user,
When I am using:
genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro
to add water in a coarse grained system, after running mdrun I am getting
Syntax error and it shows maybe the distances are so close or there are
some clashes.
Do you know how can I figure it
Dariush Mohammadyani wrote:
Dear user,
When I am using:
genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro
to add water in a coarse grained system, after running mdrun I am
getting Syntax error and it shows maybe the distances are so close or
there are some
Justin, thank you very much for your time and help. I am using pbc = xy
(with two walls, one on each side), but my box actually expands wildly,
which is very strange, rather than contracting and compressing the vacuum
regions. So I am not sure what to think. Maybe I should switch to pbc =
xyz
Yes, you are right. I made a mistake to write an error:
[n0017:07436] *** Process received signal ***
[n0017:07436] Signal: Segmentation fault (11)
[n0017:07436] Signal code: Address not mapped (1)
[n0017:07436] Failing at address: 0x1d620d20
What do you mean for Better energy minimization?
Andrew DeYoung wrote:
Justin, thank you very much for your time and help. I am using pbc = xy
(with two walls, one on each side), but my box actually expands wildly,
which is very strange, rather than contracting and compressing the vacuum
regions. So I am not sure what to think. Maybe I
Dariush Mohammadyani wrote:
Yes, you are right. I made a mistake to write an error:
[n0017:07436] *** Process received signal ***
[n0017:07436] Signal: Segmentation fault (11)
[n0017:07436] Signal code: Address not mapped (1)
[n0017:07436] Failing at address: 0x1d620d20
What do you
Mark,
My restrains on topology consist of the next section
; Include Position restraint file
#ifdef POSRES
#include posre.itp
#endif
[ dihedral_restraints ]
; ai ajakal type label phi dphi kfac power
; Chi N - CA - CB - CG
29082910 29112912 1 1 180 0
James Starlight wrote:
Mark,
My restrains on topology consist of the next section
; Include Position restraint file
#ifdef POSRES
#include posre.itp
#endif
[ dihedral_restraints ]
; ai ajakal type label phi dphi kfac power
; Chi N - CA - CB - CG
29082910 2911
Justin,
The whole error was
Reading file md_rest1.tpr, VERSION 4.5.5 (single precision)
NOTE: atoms involved in distance restraints should be within the longest
cut-of$
---
Program mdrun_mpi_d.openmpi, VERSION 4.5.5
Source code file:
James Starlight wrote:
Justin,
The whole error was
Reading file md_rest1.tpr, VERSION 4.5.5 (single precision)
NOTE: atoms involved in distance restraints should be within the longest
cut-of$
---
Program mdrun_mpi_d.openmpi, VERSION
Hi,
somebody have an idea about this?
Cheers
Sabine
On 03/09/2012 03:52 PM, Sabine Reisser wrote:
Hi everyone,
I'm trying to fold an unfolded peptide to a helix via umbrella sampling.
I've defined 21 pulling groups, the C-Alpha atoms of the peptide, and i
am restraining the distance between
Dear user,
I have a system that is contained of protein-water-ions. There, I
select the whole protein first for calculation, and then this protein
for output. I used the following command:
g_sas -f free.xtc -s free.tpr -o area -or res_area -oa
atom_area –q -nopbc
In this way I can obtain
On 3/10/12, lina lina.lastn...@gmail.com wrote:
On Sat, Mar 10, 2012 at 10:23 PM, Atila Petrosian
atila.petros...@gmail.com wrote:
Dear Lina
There is not any things related to list of atoms on the terminal.
Might your distance -dist so large.
try a smaller one and see.
Best regards
--
Hi Users:
I was trying to calculate the energy contribution of an specific ion in my
simulation. After extract a given frame from the simulation, I recalculate
the energies of this frame with mdrun -rerun. Then I used tpbconv and
editconf to create a new gro file and a new tpr without the ion. I
Hi,
I am running Gromacs 4.5.5. Can you please tell me what source code file(s)
contain the code for writing the .edr file during mdrun? The manual gives a
lot of information about how various quantities (e.g., pressure) are
calculated, but I would like to see exactly in the code where
Hi,
I have a system containing two graphene sheets (with residue names GR1 and
GR2, respectively) plus some liquid. I would like to hold the two graphene
sheets fixed in space and observe the dynamics of the liquid around it.
To hold the graphene sheets fixed in space, I used freeze groups:
On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote:
Hi Users:
I was trying to calculate the energy contribution of an specific ion
in my simulation. After extract a given frame from the simulation, I
recalculate the energies of this frame with mdrun -rerun. Then I used
tpbconv and editconf
On 15/03/2012 6:33 AM, Andrew DeYoung wrote:
Hi,
I am running Gromacs 4.5.5. Can you please tell me what source code file(s)
contain the code for writing the .edr file during mdrun? The manual gives a
lot of information about how various quantities (e.g., pressure) are
calculated, but I would
Dear All,
For the gromacs 3.3.3 and gromacs 4.5.5, for regular protein molecular dynamics
simulation, will you please tell me the possible difference on their calculated
results?
Cheers,
Fenghui--
gmx-users mailing listgmx-users@gromacs.org
On 15/03/2012 12:05 PM, Wholly Peach wrote:
Dear All,
For the gromacs 3.3.3 and gromacs 4.5.5, for regular protein molecular
dynamics simulation, will you please tell me the possible difference
on their calculated results?
In principle, not very much difference in results. Big differences
Hi, all,
Does hydrogen hydrogen non-bond interactions be calculated in the
simulation? It looks to me this kind of non-bond interaction is ignored. If
not, is there a way to let it count h-h interaction? Thank you!
Bo
--
gmx-users mailing listgmx-users@gromacs.org
bo.shuang wrote:
Hi, all,
Does hydrogen hydrogen non-bond interactions be calculated in the
simulation? It looks to me this kind of non-bond interaction is ignored.
If not, is there a way to let it count h-h interaction? Thank you!
It is common for force fields to assign zero values to
This depends on your forcefield.
Look in ffnonbonded.itp for your forcefield to see if the hydrogens have
nonzero terms. Also make sure your hydrogens have charges assigned to them
in your topology if you want electrostatic interactions to be calculated.
On 2012-03-14 09:20:28PM -0500, bo.shuang
Dear All,
Suppose I need to install the GROMACS in my laptop. Will you please tell me the
requirement on the capacity of RAM?
Cheers,
wholly--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
On 15/03/2012 2:57 PM, Wholly Peach wrote:
Dear All,
Suppose I need to install the GROMACS in my laptop. Will you please
tell me the requirement on the capacity of RAM?
That's a bit like someone asking how many bedrooms their house needs -
if you don't know how many people, then all you can
On 15/03/2012 2:50 PM, cuong nguyen wrote:
Dear Gromacs users,
I prepare to run my simulations on the supercomputer on single node
with 64 CPUs. Although I have seen on Gromacs Mannual suggesting to
use MPI to parellel, I still haven't understood how to use this
application and which commands
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