Re: [gmx-users] how to set domain decomposition for inhomogeneous systems?

[Mark Abraham]

On 5/09/2011 12:28 PM, zhongjin wrote:
Thanks for your reply, potential energy is always large and positive, 
maybe because the CNT is always freezed during the simulation process.




That would have been a good thing to describe, along with your other 
simulation conditions. Giving as much information as you think could 
possibly be relevant is much more likely to get a timely solution.


In your shoes, I would check that my nanotube is stable before I 
introduce the electrolyte.


Mark
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[gmx-users] how to set domain decomposition for inhomogeneous systems?

[zhongjin]

Thanks for your reply, potential energy is always large and positive, maybe 
because the CNT is always freezed during the simulation process.
Zhongjin -- 
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Re: [gmx-users] Question about adding hydrogens to a newly constructed residue

[Mark Abraham]

On 5/09/2011 3:30 AM, J. Nathan Scott wrote:

Hello fellow GROMACS users,

I am in the process of constructing a new residue in the OPLS-AA force 
field for the mCherry chromophore. However, I am having some 
difficulty in adding three CH3 hydrogens. In the 2H5Q PDB structure 
the chromophore residue, CH6, has CE1 and CE2 ring carbons defined, 
but also an extended chain carbon named CE. The problem is that my hdb 
rules were assigning HE1 and HE2 to the ring carbon hydrogens (1   
1   HE1 CE1 CD1 CZ for example), and HE1, HE2, and HE3 
to the CE carbon hydrogens (3   4   HE CE SD  
CG1). Since these hydrogens are of different types, I need to have 
them named distinctly in my RTP file and need for Gromacs to 
understand them as different types. I changed the CH6 residue's CE 
atom to CE3 in the PDB file and the relevant RTP entries accordingly 
(see below). I also changed the hdb entry for the new CE3 atom (also 
below).


Relevant RTP lines:
   CE3opls_209  0.0 10
  HE31opls_140  0.0 11
  HE32opls_140  0.0 12
  HE33opls_140  0.0 13
   CE1opls_145  0.0 32
   HE1opls_146  0.0 33
   CE2opls_145  0.0 34
   HE2opls_146  0.0 35
 [bonds]
   CE3  HE31
   CE3  HE32
   CE3  HE33
   CE1   HE1
   CE2   HE2

Relevant HDB lines:
3   4   HE3 CE3 SD  CG1
1   1   HE1 CE1 CD1 CZ
1   1   HE2 CE2 CD2 CZ

I thought this would cover everything, but I am receiving the 
following sort of error from pdb2gmx for each of the the three CE3 
hydrogens(pdb2gmx -f 2H5Q.pdb -o 2H5Q_processed.gro -water tip3):


"WARNING: atom HE31 is missing in residue CH6 66 in the pdb file
 You might need to add atom HE31 to the hydrogen database of 
building block CH6

 in the file aminoacids.hdb (see the manual)"

I've looked at other examples in the aminoacids.hdb file and cannot 
figure out what I am missing here, it seems like my hdb rule should be 
adding 3 type 4 hydrogens named HE31, HE32, and HE33. I am assuming 
that the other hdb rules are OK, since they seemed to work fine 
before, as indicated by examining the gro file. I would sincerely 
appreciate any help you can offer. Thank you!


I can't see a reason why that wouldn't work. However, there's no need 
for you to preserve the PDB atom name for CE. Reducing the potential for 
some atom-naming screw-up such as this is a good reason to change it (in 
both your coordinate file and .rtp entry). It will probably just work, 
or at the very least simplify further trouble-shooting.


Mark
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[gmx-users] Question about adding hydrogens to a newly constructed residue

[J. Nathan Scott]

Hello fellow GROMACS users,

I am in the process of constructing a new residue in the OPLS-AA force field
for the mCherry chromophore. However, I am having some difficulty in adding
three CH3 hydrogens. In the 2H5Q PDB structure the chromophore residue, CH6,
has CE1 and CE2 ring carbons defined, but also an extended chain carbon
named CE. The problem is that my hdb rules were assigning HE1 and HE2 to the
ring carbon hydrogens (1   1   HE1 CE1 CD1 CZ for
example), and HE1, HE2, and HE3 to the CE carbon hydrogens (3   4
HE CE SD  CG1). Since these hydrogens are of different types, I
need to have them named distinctly in my RTP file and need for Gromacs to
understand them as different types. I changed the CH6 residue's CE atom to
CE3 in the PDB file and the relevant RTP entries accordingly (see below). I
also changed the hdb entry for the new CE3 atom (also below).

Relevant RTP lines:
   CE3opls_209  0.0 10
  HE31opls_140  0.0 11
  HE32opls_140  0.0 12
  HE33opls_140  0.0 13
   CE1opls_145  0.0 32
   HE1opls_146  0.0 33
   CE2opls_145  0.0 34
   HE2opls_146  0.0 35
 [bonds]
   CE3  HE31
   CE3  HE32
   CE3  HE33
   CE1   HE1
   CE2   HE2

Relevant HDB lines:
3   4   HE3 CE3 SD  CG1
1   1   HE1 CE1 CD1 CZ
1   1   HE2 CE2 CD2 CZ

I thought this would cover everything, but I am receiving the following sort
of error from pdb2gmx for each of the the three CE3 hydrogens(pdb2gmx -f
2H5Q.pdb -o 2H5Q_processed.gro -water tip3):

"WARNING: atom HE31 is missing in residue CH6 66 in the pdb file
 You might need to add atom HE31 to the hydrogen database of
building block CH6
 in the file aminoacids.hdb (see the manual)"

I've looked at other examples in the aminoacids.hdb file and cannot figure
out what I am missing here, it seems like my hdb rule should be adding 3
type 4 hydrogens named HE31, HE32, and HE33. I am assuming that the other
hdb rules are OK, since they seemed to work fine before, as indicated by
examining the gro file. I would sincerely appreciate any help you can offer.
Thank you!

-Nathan


-- 
--
J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University
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Re: [gmx-users] how to set domain decomposition for inhomogeneous systems?

[Mark Abraham]

On 4/09/2011 7:37 PM, zhongjin wrote:

Dear GMX user,
  I am using GMX4.5.4 (double precision) to simulate electrolyte 
confined in a CNT with polarizable model. The CNT diameter is 3.0 nm 
and length is 6.0 nm. The box is 5.0*5.0 *6.0, out of CNT is nothing, 
that is to say, the system is inhomogeneous,please see it by clicking 
this link http://photo.163.com/hzj1000/list/#aid=228653982&m=0&page=1 





I think all your runs are broken, because as your potential energy is 
always large and positive. Check out 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up.


Mark
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[gmx-users] how to set domain decomposition for inhomogeneous systems?

[zhongjin]

Dear GMX user,
  I am using GMX4.5.4 (double precision) to simulate electrolyte confined 
in a CNT with polarizable model. The CNT diameter is 3.0 nm and length is 6.0 
nm. The box is 5.0*5.0 *6.0, out of CNT is nothing, that is to say, the system 
is inhomogeneous，please see it by clicking this link 
http://photo.163.com/hzj1000/list/#aid=228653982&m=0&page=1
 
As for inhomogeneous systems,we should set the spatial decomposition with option
-dd.
I use mdrun_d -deffnm nvt -v -nt 8 ,there will be errors.
starting mdrun 'cnt in water'
25 steps,    500.0 ps.
MDStep=    0/ 0 EPot: 1.12436639e+06, rmsF: 3.00e+03
MDStep=    0/ 1 EPot: 1.10979204e+06, rmsF: 5.29e+02
MDStep=    0/ 2 EPot: 1.10935838e+06, rmsF: 1.22e+02
Warning: 1-4 interaction between 97 and 101 at distance 4.724 which is larger 
than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
MDStep=    0/ 3 EPot:  nan, rmsF: 7.48e+07
MDStep=    0/ 4 EPot:  nan, rmsF: 6.88e+07
MDStep=    0/ 5 EPot:  nan, rmsF: 7.03e+07
MDStep=    0/ 6 EPot:  nan, rmsF: 7.13e+07
MDStep=    0/ 7 EPot:  nan, rmsF: 7.02e+07
MDStep=    0/ 8 EPot:  nan, rmsF: 5.91e+07
MDStep=    0/ 9 EPot:  nan, rmsF: 5.90e+07
MDStep=    0/10 EPot:  nan, rmsF: 5.91e+07
MDStep=    0/11 EPot:  nan, rmsF: 5.94e+07
MDStep=    0/12 EPot:  nan, rmsF: 5.97e+07
MDStep=    0/13 EPot:  nan, rmsF: 6.00e+07
MDStep=    0/14 EPot:  nan, rmsF: 5.58e+07
MDStep=    0/15 EPot:  nan, rmsF: 5.59e+07
MDStep=    0/16 EPot:  nan, rmsF: 5.60e+07
MDStep=    0/17 EPot:  nan, rmsF: 5.61e+07
MDStep=    0/18 EPot:  nan, rmsF: 5.61e+07
MDStep=    0/19 EPot:  nan, rmsF: 5.62e+07
step 0: EM did not converge in 20 iterations, RMS force 121.680
step 0MDStep=    1/ 0 EPot: 1.10511682e+06, rmsF: 1.57e+02
MDStep=    1/ 1 EPot: 1.10517815e+06, rmsF: 3.49e+01
MDStep=    1/ 2 EPot: 1.10515438e+06, rmsF: 8.57e+00
MDStep=    1/ 3 EPot:  nan, rmsF: 5.65e+07
MDStep=    1/ 4 EPot:  nan, rmsF: 5.29e+07
MDStep=    1/ 5 EPot:  nan, rmsF: 5.29e+07
MDStep=    1/ 6 EPot:  nan, rmsF: 5.29e+07
MDStep=    1/ 7 EPot:  nan, rmsF: 5.29e+07
MDStep=    1/ 8 EPot:  nan, rmsF: 5.29e+07
MDStep=    1/ 9 EPot:  nan, rmsF: 5.29e+07
MDStep=    1/10 EPot:  nan, rmsF: 5.29e+07
MDStep=    1/11 EPot:  nan, rmsF: 5.31e+07
MDStep=    1/12 EPot:  nan, rmsF: 5.31e+07
MDStep=    1/13 EPot:  nan, rmsF: 5.31e+07
MDStep=    1/14 EPot:  nan, rmsF: 5.31e+07
MDStep=    1/15 EPot:  nan, rmsF: 5.31e+07
MDStep=    1/16 EPot:  nan, rmsF: 5.31e+07
MDStep=    1/17 EPot:  nan, rmsF: 5.31e+07
MDStep=    1/18 EPot:  nan, rmsF: 5.31e+07
MDStep=    1/19 EPot:  nan, rmsF: 5.31e+07
step 1: EM did not converge in 20 iterations, RMS force 8.566

Received the INT signal, stopping at the next NS step
MDStep=    2/ 0 EPot: 1.10553389e+06, rmsF: 1.03e+02
MDStep=    2/ 1 EPot: 1.10551468e+06, rmsF: 1.95e+01
MDStep=    2/ 2 EPot: 1.10551473e+06, rmsF: 4.56e+00
MDStep=    2/ 3 EPot:  nan, rmsF: 7.55e+07
MDStep=    2/ 4 EPot:  nan, rmsF: 7.11e+07
MDStep=    2/ 5 EPot:  nan, rmsF: 7.10e+07
MDStep=    2/ 6 EPot:  nan, rmsF: 7.09e+07
MDStep=    2/ 7 EPot:  nan, rmsF: 7.08e+07
MDStep=    2/ 8 EPot:  nan, rmsF: 7.08e+07
MDStep=    2/ 9 EPot:  nan, rmsF: 7.07e+07
MDStep=    2/10 EPot:  nan, rmsF: 7.07e+07
MDStep=    2/11 EPot:  nan, rmsF: 7.06e+07
MDStep=    2/12 EPot:  nan, rmsF: 7.06e+07
MDStep=    2/13 EPot:  nan, rmsF: 7.06e+07
MDStep=    2/14 EPot:  nan, rmsF: 7.06e+07
MDStep=    2/15 EPot:  nan, rmsF: 7.06e+07
MDStep=    2/16 EPot:  nan, rmsF: 7.06e+07
MDStep=    2/17 EPot:  nan, rmsF: 7.06e+07
MDStep=    2/18 EPot:  nan, rmsF: 7.06e+07
MDStep=    2/19 EPot:  nan, rmsF: 7.06e+07
step 2: EM did not converge in 20 iterations, RMS force 4.560
 
However, I use mdrun_d -deffnm nvt -v -nt 2, it is OK!
Getting Loaded...
Reading file nvt.tpr, VERSION 4.5.4 (double precision)
Starting 2 threads
Loaded with Money
Making 1D domain decomposition 2 x 1 x 1
Back Off! I just backed up nvt.trr to ./#nvt.trr.2#
Back Off! I just backed up nvt.edr to ./#nvt.edr.2#
starting mdrun 'cnt in water'
25 steps,    500.0 ps.
MDStep=    0/ 0 EPot: 1.12436639e+06, rmsF: 3.00e+03
MDStep=    0/ 1 EPot: 1.10979204e+06, rmsF: 5.29e+02
MDStep=    0/ 2 EPot: 1.10935838e+06, rmsF: 1.22e+02
MDStep=    0/ 3 EPot: 1.10933788e+06, rmsF: 3.43e+01
MDStep=    0/ 4 EPot: 1.10933636e+06, rmsF: 9.99e+00
MDStep=    0/ 5 EPot: 1.10933623e+06, rmsF: 2.91e+00
MDStep=    0/ 6 EPot: 1.10933622e+06, rmsF: 8.43e-01
MDStep=    0/ 7 EPot: 1.10933622e+06, rmsF: 2.53e-0