On 24/03/2012 5:46 PM, Acoot Brett wrote:
Dear All,
Suppose I have run a 1 ns production MD. After analysis I find I need
to run another 1 ns production MD on the basis of the completed 1 ns MD.
In this way can the files by the second 2 ns production MD indicates
the MD is from 0 ns to 2 ns?
Dear All,
Suppose I have run a 1 ns production MD. After analysis I find I need to run
another 1 ns production MD on the basis of the completed 1 ns MD.
In this way can the files by the second 2 ns production MD indicates the MD is
from 0 ns to 2 ns?
Cheers,
Acoot--
gmx-users mailing lis
ahmet yıldırım wrote:
Dear user,
Please see attached file. I renumbered the "cgnr" of a ligand. Is there
any mistake related to renumbered of "cgnr"?
I see nothing unreasonable.
I get the following error when I run position restrain (pr.mdp)
mdrun -deffnm pr
Fatal error:
A charge group m
Dear user,
Please see attached file. I renumbered the "cgnr" of a ligand. Is there any
mistake related to renumbered of "cgnr"?
I get the following error when I run position restrain (pr.mdp)
mdrun -deffnm pr
Fatal error:
A charge group moved too far between two domain decomposition steps
This us
On 2012-03-23 05:39:38PM -0400, Justin A. Lemkul wrote:
>
>
> Andy Somogyi wrote:
> > Hi All,
> >
> > I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL,
> > http://viperdb.scripps.edu/info_page.php?VDB=1dzl
> >
> > using
> >
> > pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.
Andy Somogyi wrote:
Hi All,
I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL,
http://viperdb.scripps.edu/info_page.php?VDB=1dzl
using
pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top
I've tried CHARMM27 and AMBER03 FFs, water none and I get the result:
Fatal error:
At
Andrew DeYoung wrote:
Hi,
If you have time, can you please tell me if checkpoint (.cpt) files contain
data on energies?
Yes, it does.
Suppose I have a checkpoint file check.cpt, which I obtained by using the
-cpo flag of mdrun. Now suppose I want to continue the run using a new .mdp
file
Hi All,
I'm trying to generate topology for a PDB from viperdb, PDB ID 1DZL,
http://viperdb.scripps.edu/info_page.php?VDB=1dzl
using
pdb2gmx -f 1dzl_full.pdb -o test.pdb -p test.top
I've tried CHARMM27 and AMBER03 FFs, water none and I get the result:
Fatal error:
Atom CG is used in the topo
Compare and contrast with Klauda et al. Phys Chem. B, 2010, 114, 7830 ?
On 2012-03-23 02:28:45PM -0500, Krzysztof Kuczera wrote:
> Hi GMX Users,
>
> I have generated a topology entry for the DOPC lipid for
> charmm27.ff/lipids.rtp
> by copying and editing the entry of POPC. My DOPC has passed tw
Hi,
If you have time, can you please tell me if checkpoint (.cpt) files contain
data on energies?
Suppose I have a checkpoint file check.cpt, which I obtained by using the
-cpo flag of mdrun. Now suppose I want to continue the run using a new .mdp
file (not just extend it,
http://www.gromacs.org
Hi GMX Users,
I have generated a topology entry for the DOPC lipid for
charmm27.ff/lipids.rtp
by copying and editing the entry of POPC. My DOPC has passed two simple
tests
with gromacs-4.5.3 on a test structure of an isolated model molecule
(generated with CHARMM)
1) energy minimization pro
ahmet yıldırım wrote:
Dear Justin,
Thanks for your reply. You said "You should avoid ad hoc changes."
You used different parameters for energy minimization at tutorial called
"Tutorial 5: Protein-Ligand Complex".
_*a part of your em.mdp*_
nstlist = 1
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
On 24/03/2012 5:38 AM, Lara Bunte wrote:
Hello
I want to equilibrate the water around my (small) molecule. In the tutorials I
found and in the manual is not enough information how to do that if you have an
own parametrization of a molecule.
Here is my situation:
I have a pdb file and I have
Dear Justin,
Thanks for your reply. You said "You should avoid ad hoc changes."
You used different parameters for energy minimization at tutorial called
"Tutorial 5: Protein-Ligand Complex".
*a part of your em.mdp*
nstlist = 1
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
*a part of your md.mdp*
nstli
Hello
I want to equilibrate the water around my (small) molecule. In the tutorials I
found and in the manual is not enough information how to do that if you have an
own parametrization of a molecule.
Here is my situation:
I have a pdb file and I have a parametrization for this molecule out o
>
> De: David van der Spoel
>Para: Discussion list for GROMACS users
>Enviadas: Sexta-feira, 23 de Março de 2012 14:31
>Assunto: Re: [gmx-users] Charmm Cholesterol parameters - str to itp
>
>On 2012-03-23 15:31, Ricardo O. S. Soares wrote:
>> Hi GMX-users,
ahmet yıldırım wrote:
Dear users,
I am using the Reaction-Field method for electrostatics interactions. I
used the following parameters for all input files (em.mdp, pr.mdp,
nvt.mdp, npt.mdp, md.mdp). I just changed as an epsilon_rf=78 in md.mdp.
If I set nstlist=rlist=rcoulomb=rvdw=1.0 for
On 2012-03-23 15:31, Ricardo O. S. Soares wrote:
Hi GMX-users,
Klauda et al (J. Phys. Chem. B, 2012, 116(1), pp 203–210) recently
provided Cholesterol parameters for Charmm FF.
Does anyone know/have a protocol or script to convert the .str file to a
valid .itp file for Charmm within GROMACS?
I u
Dear users,
I am using the Reaction-Field method for electrostatics interactions.
I used the
following parameters for all input files (em.mdp, pr.mdp, nvt.mdp, npt.mdp,
md.mdp). I just changed as an epsilon_rf=78 in md.mdp. If I set
nstlist=rlist=rcoulomb=rvdw=1.0 for energy minimization, would no
Sabine, thanks for filing it in redmine! Having a record helps a lot.
Can you also attach all your input files to the redmine filing? It
can only really be debugged if the input files you used are included.
Best,
Michael
On Fri, Mar 23, 2012 at 9:11 AM, Justin A. Lemkul wrote:
>
>
> Sabine Rei
Hi GMX-users,
Klauda et al (J. Phys. Chem. B, 2012, 116 (1), pp 203–210) recently provided
Cholesterol parameters for Charmm FF.
Does anyone know/have a protocol or script to convert the .str file to a valid
.itp file for Charmm within GROMACS?
I understand that Dr. Spoel and colleagues (J. Am.
Acoot Brett wrote:
Dear All,
For the npt.mdp downloaded from the Justin Lemkul tutorial, it seems we
need to add a line of "refcoord_scaling*".*
If so, its value should be "all" or "com"?
I am looking forward to getting a reply from you.
Either should work. I doubt that for this cas
Dear All,
For the npt.mdp downloaded from the Justin Lemkul tutorial, it seems we need to
add a line of "refcoord_scaling".
If so, its value should be "all" or "com"?
I am looking forward to getting a reply from you.
Cheers,
Acoot --
gmx-users mailing listgmx-users@gromacs.org
htt
Sabine Reisser wrote:
Hi Mark,
with FE, without PR : same error
without FE, with PR: stable
without FE, without PR: stable
I've never had this error before.
Logfile says:
[...]
Initializing Domain Decomposition on 2 nodes
Dynamic load balancing: no
Will sort the charge groups at every domain
Gavin Melaugh wrote:
Hi all
I have a system of 40 solute molecules in a solvent of 480 crown ether
molecules. I am not trying to insert 100 methane molecules into this
relaxed and well equilibrated structure using genbox.
There are clearly visible cavities in the fluid but genbox only alllows
23 mar 2012 kl. 11.37 skrev Justin A. Lemkul:
>
>
> francesco oteri wrote:
>> I understand,
>> I am planning to run REMD between 300 and 600 K, so I think it is better
>> equlibrating in NVT ensemble because at high temperature water evaporates,
>> is it?
>
> Another very real concern is the
Hi all
I have a system of 40 solute molecules in a solvent of 480 crown ether
molecules. I am not trying to insert 100 methane molecules into this
relaxed and well equilibrated structure using genbox.
There are clearly visible cavities in the fluid but genbox only alllows
the insertion of 8 methan
ahmet yıldırım wrote:
Hi,
/quote from a paper: A twin range cut-off for van der Waals (0.9/1.4 nm)
and a smooth particle mesh Ewald algorithm for Coulomb interactions
(switching distance of 0.9 nm) were used./
i.e.this means:
; NEIGHBORSEARCHING PARAMETERS
.
rlist
Hi, Sabine-
If you can go to http://redmine.gromacs.org/projects/gromacs/issues
and file a bug report (including attaching files), I can look at it.
If that's ends up not working well, you can send me the files off of
the list, but it's usually better to have things in the redmine system
so proble
Hi Mark,
with FE, without PR : same error
without FE, with PR: stable
without FE, without PR: stable
I've never had this error before.
Logfile says:
[...]
Initializing Domain Decomposition on 2 nodes
Dynamic load balancing: no
Will sort the charge groups at every domain (re)decomposition
Initia
Hi,
*quote from a paper: A twin range cut-off for van der Waals (0.9/1.4 nm)
and a smooth particle mesh Ewald algorithm for Coulomb interactions
(switching distance of 0.9 nm) were used.*
i.e.this means:
; NEIGHBORSEARCHING PARAMETERS
.
rlist = 0.9
; OPTIONS FOR ELECTROS
On 23/03/2012 9:17 PM, Sabine Reisser wrote:
Dear gromacs users/developers,
when trying to couple in a peptide into a membrane with:
; Define position restraints for peptide
define = -DPOSRES
; couple in peptide
free_energy = yes
init_lambda = 0.05
sc_alpha= 0.7
sc_pow
francesco oteri wrote:
I understand,
I am planning to run REMD between 300 and 600 K, so I think it is better
equlibrating in NVT ensemble because at high temperature
water evaporates, is it?
Another very real concern is the stability of the simulations under NPT. At
higher temperatures
Dear gromacs users/developers,
when trying to couple in a peptide into a membrane with:
; Define position restraints for peptide
define = -DPOSRES
; couple in peptide
free_energy = yes
init_lambda = 0.05
sc_alpha= 0.7
sc_power= 1
couple-moltype = Protein
couple
I understand,
I am planning to run REMD between 300 and 600 K, so I think it is better
equlibrating in NVT ensemble because at high temperature
water evaporates, is it?
Francesco
Il giorno 23 marzo 2012 10:53, Kukol, Andreas ha
scritto:
> Hi Francesco,
>
> It should be the same ensemble, in whi
Hi Francesco,
It should be the same ensemble, in which you want to carry out the production
REMD.
Andreas
>>>
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of francesco oteri
Sent: 23 March 2012 09:41
To: Discussion list for GROMACS users
Subj
On 03/23/2012 10:41 AM, francesco oteri wrote:
> Dear gromacs users,
> I have to perform REMD simulation, but since it is the first time I apply
> this tecnique I have a question regarding system equilibration.
> As far as I know, befaore starting the REMD each replica has to be
> equlibrated. The
Dear gromacs users,
I have to perform REMD simulation, but since it is the first time I apply
this tecnique I have a question regarding system equilibration.
As far as I know, befaore starting the REMD each replica has to be
equlibrated. The equilibration has to be carried out in the NPT ensemble
o
Hi,
check
http://pubs.acs.org/doi/abs/10.1021/ct100494z
and g_wham -h
Cheers,
Jochen
Am 3/20/12 10:10 AM, schrieb Steven Neumann:
Dear Gmx Users,
Could you please write me how to evaluate the statistical error of the
binding free energy obtained by umbrella sampling?
Thank you
Steven
--
Hi,
the key
Umb. Pos. 0.0
indicates the the umbrella center of this simulaiton is at 0.0, not that
the profile should starts at zero. Beginning and end of profile are set
with -min -max.
cheers,
Jochen
Am 3/22/12 7:03 PM, schrieb rainy908:
Hi all,
I am experiencing a potential problem wi
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