Dear Marcelo:
This doesn't address your virtual sites question, but I have used a
simple oxygen model in the past and posted it to the mailing list:
http://lists.gromacs.org/pipermail/gmx-users/2009-March/040239.html
With regards to your actual query:
1) as far as I know, molecular oxygen doe
On 30/12/10 01:07, Justin A. Lemkul wrote:
It sounds very much like your systems are in the minority - those for
which -maxwarn is essential :)
Oh yes. But... you don't want to discriminate minorities!! :D
What I meant was that -maxwarn allows a user to casually bypass that
which grompp is al
ms wrote:
On 29/12/10 23:47, Justin A. Lemkul wrote:
I think the root problem boils down to a lack of documentation of this
feature. For most routine use, -maxwarn should not be used, similar to
-missing with pdb2gmx.
Yes, but it depends. In my systems I routinely have to use both to get
t
I am trying to simulate oxygen using gromacs but there seems to be no
forcefield parameters for this molecule.
So I would like to add a forcefield to gromacs which is a 3 site model:
The two oxygens are lennard jones particles and there's a point charge
at the center of mass.
The reference a
On 29/12/10 23:47, Justin A. Lemkul wrote:
I think the root problem boils down to a lack of documentation of this
feature. For most routine use, -maxwarn should not be used, similar to
-missing with pdb2gmx.
Yes, but it depends. In my systems I routinely have to use both to get
the system rig
Sounds great to me. Thanks Justin.
-- original message --
... ...
It seems that my little comment has generated quite the controversy :)
I think the root problem boils down to a lack of documentation of this
feature.
For most routine use, -maxwarn should not be used, similar to -missing
ms wrote:
On 29/12/10 21:57, chris.ne...@utoronto.ca wrote:
That sounds reasonable. I don't like hidden options except for when they
are associated with manuscripts that have not yet been published.
As a "young" Gromacs user and an "old" free software user and developer,
I wholeheartedly di
On 29/12/10 21:57, chris.ne...@utoronto.ca wrote:
That sounds reasonable. I don't like hidden options except for when they
are associated with manuscripts that have not yet been published.
As a "young" Gromacs user and an "old" free software user and developer,
I wholeheartedly disagree with h
That sounds reasonable. I don't like hidden options except for when
they are associated with manuscripts that have not yet been published.
If people want to make -maxwarn more difficult to use, it might be
possible to use one of the two following mutually exclusive options:
A) do not includ
On 30/12/2010 1:58 AM, Florian Dommert wrote:
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On 12/29/2010 12:56 AM, Mark Abraham wrote:
On 29/12/2010 7:44 AM, Justin A. Lemkul wrote:
TJ Mustard wrote:
Hi,
I am trying to speed up my parallel processor Gromacs jobs and was
wondering what w
On 30/12/2010 4:36 AM, Justin A. Lemkul wrote:
chris.ne...@utoronto.ca wrote:
Strongly disagreed. I use maxwarn all the time. If it was a hidden
option, how would I have ever known about it? Further, if it was a
hidden option, then developers would need to be very careful about
throwing warn
In addition to Justin's comments, check your convergence with block
averaging. Is there a systematic energy drift as you increase the
amount of sampling prior to each block? Also, try applying your method
to Na+ and Cl- in a box of water. If you can't get that free energy
correctly, then yo
mohsen ramezanpour wrote:
Dear All
I estimated protein-ligand free energy about -300 kj
Is it logical?I think it is wrong.what do you think?
There is no way for anyone on this list to assess such things. It sounds
unphysical to me, but that's just a gut reaction based on nothing in particu
mohsen ramezanpour wrote:
Dear All
I am using this configuration.mdp file for pulling.this is the same as
umbrella sampling,of course I have changed some parts of it
according to my problem(protein-ligand free energy).but when i use
grompp this warning is occuring.
The only reason I can see
Dear All
I estimated protein-ligand free energy about -300 kj
Is it logical?I think it is wrong.what do you think?
what is the range of correct value for a typical protein-ligand?
protein=660 residue
ligand=25 atom
water=4670
Na=118
Cl=120
thanks in advance
--
gmx-users mailing listgmx-users
Dear All
I am using this configuration.mdp file for pulling.this is the same as
umbrella sampling,of course I have changed some parts of it
according to my problem(protein-ligand free energy).but when i use grompp
this warning is occuring.
WARNING 1 [file configuration.mdp, line unknown]:
Unknown
MyLinkka wrote:
Hi Justin,
Thanks for your answer!
As far as I understood, the virial expression of pressure has two parts,
the kinetic energy contribution and the potential energy contribution.
Even when
temperature is undefined or zero, the product of pair force and distance
between
atoms
Hi Justin,
Thanks for your answer!
As far as I understood, the virial expression of pressure has two parts,
the kinetic energy contribution and the potential energy contribution. Even when
temperature is undefined or zero, the product of pair force and distance between
atoms still contribute to
Nilesh Dhumal wrote:
My box size is 4.5 4.5 4.5 (in nm)90 90 90
Seems awfully large for only 128 waters. I just wonder if the box is distorting
during the simulation such that the periodic distance becomes the reference
distance, hence the switch between positive and negative distances.
Nilesh Dhumal wrote:
I have a system with 128 water molecules and a ion pair of ionic liquids
i.e. one cation and one anion.
the reaction corrdination is the distance between cation and anion.
Initial distance between cation-anion is 0.8 nm.
What is the size of the smallest box vector?
I ha
ahmet yıldırım wrote:
OK. if I do what sort change in pdb file, there is no need to create
.rtp file. It seems difficult to create the .rtp file.
That depends on whether you need this residue, hence all of my previous
questions. If there is some functional significance to this residue and
OK. if I do what sort change in pdb file, there is no need to create .rtp
file. It seems difficult to create the .rtp file.
Thanks for your help
29 Aralık 2010 19:49 tarihinde Justin A. Lemkul yazdı:
>
>
> ahmet yıldırım wrote:
>
>> You said "You do not have to make changes in pdb file".
>>
>
>
I have a system with 128 water molecules and a ion pair of ionic liquids
i.e. one cation and one anion.
the reaction corrdination is the distance between cation and anion.
Initial distance between cation-anion is 0.8 nm.
I have pasted some part of md file
; Pull code
pull= umbrella
pul
Nilesh Dhumal wrote:
If I am geting -ve value if z in g_wham then zero is my initial distance
or reference distance.
That means your pull group has a coordinate that is negative with respect to the
reference group at some point during (at least) one of the umbrella sampling
windows. Zero,
ahmet yıldırım wrote:
You said "You do not have to make changes in pdb file".
When did I say that?
Then How will I create .rtp file.
That depends entirely upon what that residue is. Is it a constituent residue of
the protein, such that its backbone is incorporated in the protein struct
You said "You do not have to make changes in pdb file".
Then How will I create .rtp file.
29 Aralık 2010 19:32 tarihinde Justin A. Lemkul yazdı:
>
>
> ahmet yıldırım wrote:
>
>> Dear Justin,
>>
>> Thanks for your reply. Where is the error?
>>
>> Pdb file:
>>
>> ATOM 1 N ALA A 4
>> ATOM
If I am geting -ve value if z in g_wham then zero is my initial distance
or reference distance.
Nilesh
On Sat, December 11, 2010 9:43 pm, Justin A. Lemkul wrote:
>
>
> Nilesh Dhumal wrote:
>
>> Hello,
>> I trying to run umbrella sampling simulation for system.
>>
>>
>> After running g_wham comma
chris.ne...@utoronto.ca wrote:
Strongly disagreed. I use maxwarn all the time. If it was a hidden
option, how would I have ever known about it? Further, if it was a
hidden option, then developers would need to be very careful about
throwing warnings only in the most dire situations because th
ahmet yıldırım wrote:
Dear Justin,
Thanks for your reply. Where is the error?
Pdb file:
ATOM 1 N ALA A 4
ATOM 2 CA ALA A 4
ATOM 2688 N ALA B 4
ATOM 2689 CA ALA B 4
ATOM 5449 OXT GLN B 361
TER5450 GLN B 361
Right here. You're going from
Dear Justin,
Thanks for your reply. Where is the error?
Pdb file:
ATOM 1 N ALA A 4
ATOM 2 CA ALA A 4
ATOM 2688 N ALA B 4
ATOM 2689 CA ALA B 4
ATOM 5449 OXT GLN B 361
TER5450 GLN B 361
HETATM 5451 OAAABSG A 1
HETATM 5452 OABABSG A 1
ahmet yıldırım wrote:
Dear Mark,
The chain identifier have continuous. In sequence does not show any problem.
Then you're not looking at the right contents; pdb2gmx wouldn't complain
otherwise. Usually HETATM entries like HOH (water) are after all protein
chains, so you might have chain
Dear Aswathy:
The answer depends on how you did the pulling. Did you do umbrella
sampling or non-equilibrium pulling? Please post your .mdp option.
Also, in my opinion, running a simulation before you are sure how to
post-process the data is a recipe for wasting cpu cycles. Preferably,
on
Strongly disagreed. I use maxwarn all the time. If it was a hidden
option, how would I have ever known about it? Further, if it was a
hidden option, then developers would need to be very careful about
throwing warnings only in the most dire situations because the general
user would not know
Dear Mark,
The chain identifier have continuous. In sequence does not show any problem.
29 Aralık 2010 15:10 tarihinde Mark Abraham yazdı:
> On 29/12/2010 10:12 PM, ahmet yıldırım wrote:
>
>> Dear users,
>>
>> a...@ubuntu:~/Desktop/3O87$ pdb2gmx -f 3O87.pdb -water tip3p
>>
>> Select the Force
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On 12/29/2010 12:56 AM, Mark Abraham wrote:
> On 29/12/2010 7:44 AM, Justin A. Lemkul wrote:
>>
>>
>> TJ Mustard wrote:
>>>
>>>
>>> Hi,
>>>
>>>
>>>
>>> I am trying to speed up my parallel processor Gromacs jobs and was
>>> wondering what were the known
Dear all,
I have met a problem in my simulation, where I hope to remove the
center of mass of one group, namely CNT02, and to pull another group
by a constant force. My mdp file reads:
; Remove center of mass translation
comm_mode = Linear
nstcomm = 10
comm_grps
mina Madah wrote:
Dear all
if the gromacs isn't adequate for simulation of BCN graphen , I'd like
to know which simulation package/program is better for this work?
pleas suggest me about it.
Gromacs is perfectly capable of simulating just about anything, but the problem
lies in the fa
Dear all
if the gromacs isn't adequate for simulation of BCN graphen , I'd like to know
which simulation package/program is better for this work?
pleas suggest me about it.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please s
On 29/12/2010 11:06 PM, mina Madah wrote:
dear all user
How can I have a force field for simulation of boron-nitride-carbon (BCN)
graphene?
all force field in gromacs don't have boron as an atomtype .
That's because those forcefields are primarily aimed at biochemistry
simulations. You need
On 29/12/2010 10:12 PM, ahmet yıldırım wrote:
Dear users,
a...@ubuntu:~/Desktop/3O87$ pdb2gmx -f 3O87.pdb -water tip3p
Select the Force Field:
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
Fatal error:
Chain identifier 'A' was used in two non-sequential blocks (residue
710, ato
dear all user
How can I have a force field for simulation of boron-nitride-carbon (BCN)
graphene?
all force field in gromacs don't have boron as an atomtype .
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive a
Dear users,
a...@ubuntu:~/Desktop/3O87$ pdb2gmx -f 3O87.pdb -water tip3p
Select the Force Field:
5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
Fatal error:
Chain identifier 'A' was used in two non-sequential blocks (residue 710,
atom 54 49)
What should I do to correct this error?
On 29/12/2010 6:33 PM, delara aghaie wrote:
Dear Justin
many thanks for your email and your comments.
I found aminoacids.dat in the following pat
*/apps/gromacs/4.0.5/share/gromacs/top*
I connect to imerial college via vpn. they have installed several
gromacs versions.
I only write
*module loa
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