Dear GMXers,
I have a quad-core computer at hand, on which I would like to install a
parallel implementation of GMX-4.5.1. The homepage
(http://www.gromacs.org/About_Gromacs/Release_Notes/Version_4.5) refers to
"running on a multi-core node now uses thread-based parallelization to
automatic
Dear gmx users,
I am performing a MD simulation of a polymer film using GROMACS-4.0.7. My
computer has a four-core CPU, which enables the parallel implementation. At
first, I used mpimdrun to simulate the system, only to find with -v that the
vol is too small (about 0.2) and the imb F is too
Dear gmx users,
I am performing one MD simulation of a polymer system using GROMACS-4.0.7. I
want to calculate the cohesive energy. According to the definition, cohesive
energy can be calculated the difference in energy between the model system with
and without pbc. I must perform the two se
Dear GMXers,
When I perfomed a MD simulation, it always teminated after about 700 ps with
the message:
Fatal error: 2 particles communicated to PME node 0 are more than a cell length
out of the domain decomposition cell of their charge group
I utilized the GROMACS-4.0.5. I have searched
+1100
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] a bit strange errors
>
> wuxiao wrote:
> > Dear GMXers,
> > Recently, I has been performing coarse-grained MD simulations based
> > on the tabulated potentials using GROM
are given, which lead to
terminate the simulation. Are there any other reasons responsible for it?
Best wishes,
Chaofu Wu, Dr.
> Date: Fri, 16 Oct 2009 14:18:17 +1100
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] a bit strange errors
>
ate: Fri, 16 Oct 2009 14:18:17 +1100
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] a bit strange errors
>
> wuxiao wrote:
> > Dear GMXers,
> > Recently, I has been performing coarse-grained MD simulations based
> > on the ta
given, which lead to
terminate the simulation. Are there any other reasons responsible for it?
Best wishes,
Chaofu Wu, Dr.
> Date: Fri, 16 Oct 2009 14:18:17 +1100
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] a bit strange errors
>
Dear GMXers,
Recently, I has been performing coarse-grained MD simulations based on the
tabulated potentials using GROMACS. In the initialization, some warnings are
given as follows
WARNING: For the 999 non-zero entries for table 0 in table_b0.xvg the forces
deviate on average 164% from m
Dear GMXers,
I have a bit puzzle about the use of nexcl. In order to calculate the
intermolecular g_rdf, the tpr file obtained from a top file is provided with
the option -s. So the nexcl in the top file would effect the result of g_rdf.
Suppose the nexcl is 3, whether are the two atoms sep
Dear GMXers,
I want to calculate the inter- and intra-molecular radial distribution
functions (rdfs), separately. However, I find the g_rdf routine can only be
useful to calculate the total rdf. Is there any similar routine which can be
used to reach my aim? Please give me some hints. Thanks
Dear GMXers,
Is there anybody who use the g_fg2cg routine for mapping and reverse-mapping
coarse-grained model on all-atom model? I want to know how it works, i.e.
whether is the center of mass of a group of atoms used as superatom? How is the
atomistic detail reintroduced to coarse-grained
Dear Gustavo,
Firstly, I suggest you put the question into this maillist to benefit all
other users. Your problem is practically the same to mine posted previously.
Generally, this can be due to the bad initial configuration. When I use long
NVT MD then NPT MD, all works very well. So I advi
Date: Mon, 21 Sep 2009 05:08:45 + (GMT)
From: Mark Abraham
Subject: Re: [gmx-users] errors due to genbox
To: Discussion list for GROMACS users
Message-ID:
Content-Type: text/plain; charset="utf-8"
On 09/21/09, wuxiao wrote:
>
>
> .hmmessage P{mar
Dear GMXers,
I try to generate gro file using genbox, but fail with some errors. Command
lines are:
genbox -ci B.gro -o Bb.gro -nmol 200 -box 3 3 3
where B.gro is the coordinate file of vinyl alcohol residue.
The errors are given as bellows. Please give me some hints to cope with
Dear GMXers,
I want to use tabulated interaction functions for bonds and angles. According
to the manual, f(x) and f'(x) should be computed as functions of x in spacing
distance of dx. For bonds, the spacing distance can be set as 0.002 (in single
precision) at default. But for angles, what
Dear GMXers,
For long time, I have had a puzzle: while the top file generally describe
interactions in a molecule, intermolecular interactions are not explicitly in
the top file. How are these intermolecular interactions described in GROMACS?
Thanks a lot for any reply.
Sincerely,
C
Dear GMXers,
by looking through the manual, I find that the tabluated interaction
functions seem very flexible for performing MD simulations. But some questions
puzzle me too much:
for bonded interactions, as for bonds, angles, dihedrals, the f'(x) are the
derivations of f(x) respective
Dear users,
I have obtained some property as function of simulation time. I want to do
running average and block average over the time. Are there some free program
for doing both works. Noted that xmgrace can do running average but can not do
block average. Thanks a lot for any reply.
Bes
Dear Mark and Vitaly,
In order to get help, here I describe the more detailed procedure.
I successfully generated the gro and top files using pdb2gmx.
pdb2gmx -f -o -p -ter
And also the grompp finished successfully.
grompp -f -c -p -o
Then I ran the mdrun in parallel way, only to fin
Dear users,
Recently, I encounter a very strange thing while perfoming MD using GROMACS.
With the same minimization parameters, mdrun can generate different
configuration in parallel way or not. It seems that the former one leads to
obvious exploding of the configuration into parts whereas
Dear gmx users,
By trials, I find a strange thing: After some energy minimizations (EM) in
parallel, steep and cg, the system would explode into parts
unexpectedly(between parts, long distance does not facilitate formation of
covalent bonds as should); However, while running EM not in parall
Dear gmx users,
I want to study polyamide using OPLS-AA force field. But for the residues,
-CH2-C(=O)-NH-CH2, I can not find suitable atom types for C, H, atoms on both
sides. I wonder whether OPLS-AA can model this kind of polymers. Could you give
me the answer? If it is, what are they? Tha
Dear gmx users,
Through the manual, I learn of that both pdb2gmx and protonate can add H
atoms according to the hdb files. About it, I have some puzzles as follows:
Are the two programs equivalent in adding H atoms? If it is yes, why bother
to develop another program? It seems that proton
Dear colleagues,
I use PME to consider coulomb interactions. It seems that the fourierspacing
is an important parameter. When it is set a larger value, the calculation can
be much faster. But what is the disadvantages of using a larger value? I wish
to get you help.
Best Regards,
Chaofu
Dear Tsjerk and other gmx users and developers,
I use OPLS-AA force field to model a dendrimer PAMAM. And the addition of
hydrogens is found correct. The rtp files were written for the core, middle and
end repeating units, respectively. The both repeating units cause the problem.
When I del
Dear gmx users,
I try to generate gro and top files using pdb2gmx, and this procedure finishs
without any error. However, when I run grompp from these files, many errors are
encountered such as:
..
ERROR 124 [file g04.top, line 20027]
No default Ryckaert-Bell. types
..
Dear gmx users,
According to the manual, Ifdef option can be used in the top file. One
question comes to me as the letter title indicates since the top file can
generate from the rtp file. Please give me the answer?
Sincerely,
Chaofu Wu
__
Dear gmx users,
While I am running grompp, many errors are identified as follows:
Error 124 [file **.top, line ]
No default Ryckaert-Bell types
What happened to this? How to cope with this problem?
Any reply would be acknowledged very much.
Sincerely
Chaofu Wu
Dear gmx users,
Can N(CH2)3 be set a charge group? Is it too large to set? Any reply would be
thanked very much.
Sincerely
Chaofu Wu
_
打工，挣钱，买房子，快来MClub一起”金屋藏娇”！
http://club.msn.cn/?from=10___
Dear Mark and gmx users,
Thanks again for attention.
Mark wrote:
>1) Geometrically large charge groups affect the group-based
>neighbour-searching problem. Electrically non-integral charge groups
>affect the accuracy of cut-off based electrostatic models. See sections
>in the manual chapter
? Also to set all of them manually is not a trivial thing.
My question (3) becomes: How to do so?
Sincerely
Chaofu Wu
--
wuxiao wrote:
> Dear gmx users,
> Recently, some questions puzzle me too much. While readin
Dear gmx users,
Recently, some questions puzzle me too much. While reading many resources, I
can not think out. Therefore, I would like to turn for this mail-list. These
questions are as follows:
(1) The total number of partial atom charge by summing the residue must be
zero?
(2) I
Dear gmx users,
In order to get more direct help, some words need to be added to the question
for the first time.
The dendrimer I want to study is just PAMAM, ethylenediamine (EDA) cored and
amine surface poly(amidoamine). The pdb file for the PAMAM has assumed to be
obtained, and I want
Dear gmx users,
On current, I plan to study a dendrimer (like PAMAM) using MD simulations
available in GROMACS. As is well-known, the .gro and .top files are the start
points for running MD simulations in GROMACS. However, the question how to
obtain the files for dendrimers puzzles me too mu
Dear gmx users,
I have performed NPT MD simulations and achieved a trr file. Now I want to
start another NVT MD simulations using some frame as the initial configuration.
But I was puzzled by how to abstract any frame from the trajectory file and to
save it as a gro file. Please give me some
Dear Song,
I guess that the problem you encountered does not matter the GROMACS. On
contrary, I think that you must have edited the pdb file and made mistakes of
the file format so that pdb2gmx can not tell it correctly. I wish this
information can help you to deal with the problem.
xiao
Dear gmx users,
If -v was passed on to mdrun, such rows one by one would be printed
continuously as follows:
vol 0.95 imb F 1% step 1000, will finish Thu Apr 30 15:39:33
Obviously, the words "step 1000, will finish Thu Apr 30 15:39:33" mean that
the current running step is 1000, the whol
Dear gmx users,
Usually, we perform NPT MD to achieve optimized density of system and start
another NVT MD to calculate other properties of interest. I think there are
three possible ways to choose the structure to start another NVT MD:(1) the
structure of last step in NPT MD trjectory;(2)t
slowly. when I using cutoff
instead of PME for columbic force, and change the cutoff from 1.4 to 1.0, the
mdrun finished 300 ps successfully. Another 3ns is started to try whether it
can succeed too. more help from these descriptions?
Best regards,
xiaowu
wuxiao wrote:
> Dear Mark,
> Thank y
:41:30 +1000
From: Mark Abraham
Subject: Re: [gmx-users] Re:The X-size of the box times triclinic skew
factor
To: Discussion list for GROMACS users
Message-ID: <49f4486a.3000...@anu.edu.au>
Content-Type: text/plain; charset=GB2312
wuxiao wrote:
> Dear Mark,
> Thank you for your reply.
CPU. Can you give more help according to these descriptions?
Best regards,
xiaowu
wuxiao wrote:
> >Dear gmx users,
> >While doing a NPT molecular dynamics(MD), A fatal error was given:
> >The X-size of the box times triclinic skew factor is smaller than the
> >numb
Dear gmx users,
While doing a NPT molecular dynamics(MD), A fatal error was given:
The X-size of the box times triclinic skew factor is smaller than the number
of DD cells times the smallest allowed cell size.
However, either NVT or NVE MD can work well. Can you give any help to deal
Hi,
I would like to perform some MD simulations for polymeric system using
GROMACS. Only to find that none of the existing force fields is suit to my
system. Fortunately, the force field functions and the coresponding parametes
have been published. So an idea comes to me that whether I can a
Hi, everybody,
I am a freshman for using GROMACS. I used to do simulations using Materials
Studio. Now I notice that versatile analysis tools are present in GROMACS, so I
decide to turn for GROMACS. I have built some polymeric structures using the
Amorphous Cell module in Materials Studio4.0. C
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