Dear Gromacs Users,
I am was wondering if I would be able tweak my simulation to run it
a bit faster. According to the chapter 3.17 of the manual, I have setup
the cut-offs and Fourier grid spacing so that the PME load is around 25%.
However, Gromacs still complains in the log file about the perfo
Hi,
For systems with vacuum the automatic domain decomposition setup does
not do a good job. It currently decomposes based on the box dimensions,
not on the actual atom distribution in the box.
I was thinking of improving this a bit for 4.1.
I would guess -dd 4 2 1 will give the best performance
On Fri, Aug 14, 2009 at 10:50:29AM +0200, Berk Hess wrote:
>
> Hi,
>
> For systems with vacuum the automatic domain decomposition setup does
> not do a good job. It currently decomposes based on the box dimensions,
> not on the actual atom distribution in the box.
> I was thinking of improving th
Lili Peng wrote:
Hi David,
Thanks for your comments. There is a group that has developed force
field parameters for the Indium(III)-DTPA using Amber:
http://www.ncbi.nlm.nih.gov/pubmed/11559086 . Since the authors were
able to successfully determine force field parameters for Amber, a
mole
Dear All,
I am new to molecular dynamics, had some tutorials and could run
some initial tests successfully in that they finished without errors
(now to analyze if results make sense).
Now my challenge is to make a molecular dynamics of a homohexamer
which binds to a ssDNS and a co-f
I follow some of the step of
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I
omitted the change in the .hdb file because I don't have explicit
hydrogens). Well, I build a polymer with 3 units. The head (H), one repeat
unit (R)and tail (T) for the polymer (H-R-T) and this
nicegromacs wrote:
I follow some of the step of
http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html (I
omitted the change in the .hdb file because I don't have explicit
hydrogens). Well, I build a polymer with 3 units. The head (H), one
repeat unit (R)and tail (T) for the po
Could anyone give me the proper procedure for adding a residue? (Using itp)
From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul
Sent: Thu 8/13/2009 1:51 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Adding a residue
Smith, C
Smith, Chanel Chonda wrote:
Could anyone give me the proper procedure for adding a residue? (Using itp)
http://oldwiki.gromacs.org/index.php/Tutorials#General
See the drug-enzyme tutorial, but be advised that PRODRG topologies often
contain unsatisfactory charges and charge groups, requir
Hi Justin,
the pdb file:
HETATM1 CAA DRG 1 83.043 46.127 36.820
HETATM2 CAB DRG 1 82.411 45.765 35.421
HETATM3 CAC DRG 1 81.495 46.822 34.598
HETATM4 CAD DRG 1 80.621 46.369 33.071
HETATM5 CAE DRG 1 79.305 47.302 32.
All of your residue numbers are one, so I think pdb2gmx is trying to make them
all one residue. Try giving each unit a sequential residue number.
-Justin
nicegromacs wrote:
Hi Justin,
the pdb file:
HETATM1 CAA DRG 1 83.043 46.127 36.820
HETATM2 CAB DRG 1 82.4
Hi Justin,
ups!! I am sorry this is the exact .pdb file.
HETATM1 CAA DR0 1 83.043 46.127 36.820 1.00 0.00
HETATM2 CAB DR0 1 82.411 45.765 35.421 1.00 0.00
HETATM3 CAC DR0 1 81.495 46.822 34.598 1.00 0.00
HETATM4 CAD DR0 1 80.621
The problem is in how you handle impropers. From your previous post, your [DRG]
entry had the following:
[ impropers ]
CAG CAF -CAM C
-CAM -CAN -CAI C
CAJ CAI OAL O
CAN CAM OAP O
CAI CAH CAJ C
The last column needs to correspond to an actual atom name; there may also be
Hi Justin,
Ok, I have done some arrangements to the .rtp file (whit the same pdb file
DR0-DRG-DRG-DR1) but I still have the same error.
the rtp file is:
[ DRG ] ;
[ atoms ]
CAA CH30.000 1
CAB CH20.000 1
CAC CH20.000 1
CAD CH20.000 1
CAE CH2
nicegromacs wrote:
Hi Justin,
Ok, I have done some arrangements to the .rtp file (whit the same pdb
file DR0-DRG-DRG-DR1) but I still have the same error.
Using these .rtp entries with the .pdb file you posted (after adjusting the
residue names) works for me, using version 4.0.5. Do you
Hi,
I am running GROMACS 4.0.5 on a peptide composed of 10 serine
residues in a water box.
During the run, there have been several pairs of files being written
into the working directory, for example:
step20230b_n5.pdb
step20230c_n5.pdb
When I look at the files in PyMo
Warren Gallin wrote:
Hi,
I am running GROMACS 4.0.5 on a peptide composed of 10 serine
residues in a water box.
During the run, there have been several pairs of files being written
into the working directory, for example:
step20230b_n5.pdb
step20230c_n5.pdb
When I lo
Dear all,
I have questions regarding the position restrain md. I tried to find the
answer of my questions from the mailing list, but it is not clear yet.
In the fws tutorial when it says (in the pr.mdp)
tc_grps=Protein non-protein
(1) Doesn't that mean everything in the system? I think for this c
Jamie Seyed wrote:
Dear all,
I have questions regarding the position restrain md. I tried to find the
answer of my questions from the mailing list, but it is not clear yet.
In the fws tutorial when it says (in the pr.mdp)
tc_grps=Protein non-protein
(1) Doesn't that mean everything in the syste
Hi Mark,
Thanks for the answers. One question still remains for me: in the fws
tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run
grompp followed by mdrun... Am I missing some thing? Because I can not see
it introduces something that to be restrained..?? Would you please let m
Jamie Seyed wrote:
Hi Mark,
Thanks for the answers. One question still remains for me: in the fws
tutorial for PR step it only uses the pr.mdp (define = -DPOSRES) and run
grompp followed by mdrun... Am I missing some thing? Because I can not see
it introduces something that to be restrained..?? W
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