Re: [gmx-users] Plotting Energies versus time

[Mark Abraham]

- Original Message -
From: "Justin A. Lemkul" 
Date: Friday, June 18, 2010 23:55
Subject: Re: [gmx-users] Plotting Energies versus time
To: Discussion list for GROMACS users 

> 
> 
> Rabab Toubar wrote:
> >Hi,
> >
> >I want to extract the values for potential E, kinetic E, total 
> E, and temperature from the log file so as to plot them versus 
> time. In NAMD it is easy to do that using cat |grep, is there a 
> similar way to do it in GMX
> >
> 
> That's what g_energy is for.

Indeed. Perhaps Rabab would learn quite a few things about how GROMACS 
workflows work by looking through some tutorial material. This lesson must be 
in at least one of them. :-)

Mark

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Re: [gmx-users] Charmm force field with gromacs

[Justin A. Lemkul]

Lennart Nilsson wrote:

Hi Justin,

 


In brief:

In practice there is only one CHARMM forcefield - all components work 
together;  the components happen to have numbers corresponding to the 
 most recent version of CHARMM at the time this particular component was 
produced. The lipid and sugar components of the forcefield have, quite 
naturally, been evolving more rapidly than the protein (stable since 
~1993) and nucleic acid (stable since ~2000) components. So, CHARMM22 
for proteins and CHARMM27 for nucleic acids refer to different 
components of the SAME forcefield.  There is also an older protein 
forcefield, CHARMM19, which is not all-atom.


 

I hope that the crew who ported the CHARMM forcefield to GROMACS 
understands this.




Thanks for the explanation.  I'm sure the developers knew what they were doing, 
and hopefully my inarticulate reply doesn't cause anyone to question their 
knowledge.  What I was hoping to make clear was that any user searching for a 
specific force field should simply be aware of what they're actually using.  The 
Perl scripts contributed to Gromacs worked with a few parameter sets several 
years ago, and the git code provides CHARMM27 so the two approaches proposed in 
the original post do not correspond to strictly the same result.  Generic 
terminology is all too often thrown around, even in the literature 
unfortunately, like "we used the Gromos force field" or "the standard Gromacs 
force field," a term which is very misleading.  In hoping to enlighten someone 
else, I too have been duly informed :)


-Justin

 


Best wishes,

Lennart Nilsson



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] building up a long polymer chain

[Justin A. Lemkul]

Moeed wrote:



for PE. or maybe this dies not affect the results since charges and mass 
are the same..?!




You can set the charges to whatever you want them to be, so this is no issue at 
all.

Also: can opls_157 be used for both CH3 & CH2,on PE chain? what is the 
suitable atom type for carbon atoms on PE chain?




The nonbonded parameters (sigma and epsilon) for opls_135 and opls_157 are 
identical.  I don't know why there are different types, but they are the same. 
Check ffoplsaanb.itp and you will see.




The top file I got has contains exactly the same listing of [bonds] 
[pairs] [angles] [dihedrals] as the one I got from the structure file 
for which I did the numbering by hand. But I am unsure of the forcefield 
parameters if they are extracted from itp file properly because after 
doing energy minimization step I get LINCS error.




I don't fully understand what you did or what you think is wrong, but I do 
recall giving you some very thorough procedures to go through to diagnose a 
crashing system.  I even updated the wiki to keep track of all the tips I gave you.






Q 2-1 Please kindly furnish me with your comments on this issue. *I need 
a residue for internal ethylene monomer in rtp file which depends as 
less as possible on atoms numbering (H11,...). *I think the solution 
will help many gmx users dealing with polymers. what would be the best 
approach?




To build a long polymer chain, it should be possible by generating a coordinate 
file of one monomer that is aligned with one of the principal axes and 
positioned such that its atoms are half a bond length from the edges of the box. 
 Then use genconf -nbox to replicate this system in one direction and you'll 
have as long a chain as you want, correctly numbered and named, and if you've 
done your geometry right, the structure will even be in a reasonable configuration.


If you want to use .rtp files to create a topology, atom naming is required to 
be consistent with the structure file.  There is no way around this.  The 
hydrogen atoms are actually very easy to deal with if you have an appropriate 
.hdb file, which is provided in the example you've been using for several weeks 
now.  So you really don't even need H atoms in your input file, just 
appropriately-named carbons.



my current internal repeating unit has numbering of atoms:
[Eth ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1-C2
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2+C1

Q 2-2. Does x2top command have advantage over pdb2gmx command with 
regards to atom numbering?




It seems like your first real problem is creating a properly-formatted 
coordinate file.  If you have to add in residue names yourself and rename all of 
the atoms yourself, then that's more trouble than its worth.  See the above 
comment about genconf.


-Justin


Many many thanks,
Best,
Moeed



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] building up a long polymer chain

[Moeed]

Dear experts,

For hexane molecule I used atom types

opls_157   12.01100  ; all-atom C: CH3 & CH2, alcohols
opls_158   12.01100  ; all-atom C: CH, alcohols

in residue file:

[ HEX ]
 [ atoms ]
C1   opls_157-0.180  1
H11  opls_140 0.060  1
H12  opls_140 0.060  1
H13  opls_140 0.060  1
C2   opls_158-0.120  2
H21  opls_140 0.060  2
H22  opls_140 0.060  2
C3   opls_158-0.120  3
H31  opls_140 0.060  3
H32  opls_140 0.060  3
C4   opls_158-0.120  4
H41  opls_140 0.060  4
H42  opls_140 0.060  4
C5   opls_158-0.120  5
H51  opls_140 0.060  5
H52  opls_140 0.060  5
C6   opls_157-0.180  6
H61  opls_140 0.060  6
H62  opls_140 0.060  6
H63  opls_140 0.060  6

now that I am trying to create top file for polyethylene (PE) I doubt if I
pickec right atom types for hexane since I see in ffoplsaa.atp file:

opls_135   12.01100  ; alkane CH3
 opls_136   12.01100  ; alkane CH2

for alkanes. Please let me know if I am right and I should use

opls_157   12.01100  ; all-atom C: CH3 & CH2, alcohols
opls_158   12.01100  ; all-atom C: CH, alcohols

for PE. or maybe this dies not affect the results since charges and mass are
the same..?!

Also: can opls_157 be used for both CH3 & CH2,on PE chain? what is the
suitable atom type for carbon atoms on PE chain?

2- I spent alot of time finding a solution for the following problem: I am
trying to build up a very long PE chain. to do this I am using the following
residues in rtp file:

; Polyethylene - this is an internal residue
[ Eth ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1-C2
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2+C1

; Terminal PE residue ("beginning" of chain)
; designation arbitrary, C1 is -CH3
; designation arbitrary, C1 is -CH3
[ EthB ]
 [ atoms ]
   C1opls_135-0.1801
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   H13   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1H11
   C1H12
   C1H13
   C1C2
   C2H21
   C2H22
   C2+C

; Terminal PE residue ("end" of chain)
; designation arbitrary, C2 is -CH3
[ EthE ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_135-0.1802
   H21   opls_140 0.0602
   H22   opls_140 0.0602
   H23   opls_140 0.0602
 [ bonds ]
   C1-C
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2H23

However, the software I am using(Ascalaph Desingner) to build up PE chain
lists atoms as shown below: (I changed the res names to Eth and EthB
myself). i.e. atoms have no numbering meaning that if I want to use the
above resudies in rtp file I will have to go thorough the whole structure
file(below) and do the numbering by myself (H to H11, H12, H21, H22...)and C
to C1 C2) which is a tedious work. when I want to generate a molecule of
4 Mw (about 1400 monomer units! or about 8000 atoms)

HETATM1  CB  EthB1   2.739   2.554  -0.012  0.00 -0.39
C
HETATM2  H   EthB1   2.736   3.644  -0.012  0.00  0.13
H
HETATM3  H   EthB1   2.190   2.217  -0.893  0.00  0.13
H
HETATM4  H   EthB1   2.190   2.217   0.868  0.00  0.13
H
HETATM5  C   Eth 2   4.155   1.993  -0.012  0.00 -0.26
C
HETATM6  H   Eth 2   4.696   2.362  -0.887  0.00  0.13
H
HETATM7  H   Eth 2   4.696   2.362   0.862  0.00  0.13
H
HETATM8  C   Eth 3   4.163   0.470  -0.012  0.00 -0.26
C
HETATM9  H   Eth 3   3.623   0.101   0.862  0.00  0.13
H
HETATM   10  H   Eth 3   3.623   0.101  -0.887  0.00  0.13
H
HETATM   11  C   Eth 4   5.579  -0.091  -0.012  0.00 -0.26
C
HETATM   12  H   Eth 4   6.119   0.278  -0.887  0.00  0.13
H
.
.
I numbered 350 atoms (60 monomer units) and simulation is working now.
56
1EthBC11   0.860   2.362   1.500
1EthB   H112   0.860   2.471   1.500
1EthB   H123   0.805   2.329   1.412
1EthB   H134   0.805   2.329   1.588
1EthBC25   1.002   2.306   1.500
1EthB   H216   1.056   2.343   1.412
1EthB   H227   1.056   2.343   1.587
2Eth C18   1.002   2.154   1.500
2EthH119   0.948   2.117   1.587
2EthH12   10   0.948   2.117   1.412
2Eth C2   11   1.144   2.098   1.500
2EthH21   12   1.198   2.135   1.412
2EthH22   13   1.198   2.135   1.587
3Eth C1   14   1.145   1.946   1.500
3EthH11   15   1.091   1.909   1

Re: [gmx-users] Thermodynamic State of SPC/E bulk water, by genbox

[David van der Spoel]

On 2010-06-18 20.22, Sikandar Mashayak wrote:

I am concerned about the number density of water. At T = 300 K and P = 1
atm, SPC/E water has certain number density (no. of molecules/nm^3).
With genbox I get .gro file with 34.04 molecules/nm^3 number density,
which will remain constant even if I do equilibration in NVT simulation
set up. So does that 34.04 molecules/nm^3 corresponds to thermodynamic
condition of water at 300K and 1 atm.

If you want to do NVT production, you still need to do an NPT 
equilbration, and extract the average density, otherwise your pressure 
will not be 1 atm in NVT.



thanks
sikandar

On Fri, Jun 18, 2010 at 12:20 PM, David van der Spoel
mailto:sp...@xray.bmc.uu.se>> wrote:

On 2010-06-18 18.24, Sikandar Mashayak wrote:

Hi

When a bulk SPC/E water box(.gro) is created using the command
"genbox
-cs spc216.gro -box 4.0 4.0 4.0", what is the thermodynamic
condition of
water?

Is it 300K at 1atm?

thanks
sikandar

No. You have to equilibrate because the box is not completely full.

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se 
http://folding.bmc.uu.se
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] Charmm force field with gromacs

[Justin A. Lemkul]

Sai Pooja wrote:


Hi,
 
I need to use charmm22 all atom force field with gromacs. What would be 
the best way to do this?

a) Use perl scripts


If you want CHARMM22, you'll have to implement it yourself.  This may require 
the use of the Perl scripts that are somewhere on the Gromacs site, but those 
are somewhat old and the code and/or file formats may have changed.



b) Use a git version in which charmm is implemented
 


The git version provides CHARMM27, I believe.

-Justin


Pooja
--
Quaerendo Invenietis-Seek and you shall discover.



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Thermodynamic State of SPC/E bulk water, by genbox

[Sikandar Mashayak]

I am concerned about the number density of water. At T = 300 K and P = 1
atm, SPC/E water has certain number density (no. of molecules/nm^3). With
genbox I get .gro file with 34.04 molecules/nm^3 number density, which will
remain constant even if I do equilibration in NVT simulation set up. So does
that 34.04 molecules/nm^3 corresponds to thermodynamic condition of water at
300K and 1 atm.

thanks
sikandar

On Fri, Jun 18, 2010 at 12:20 PM, David van der Spoel
wrote:

> On 2010-06-18 18.24, Sikandar Mashayak wrote:
>
>> Hi
>>
>> When a bulk SPC/E water box(.gro) is created using the command "genbox
>> -cs spc216.gro -box 4.0 4.0 4.0", what is the thermodynamic condition of
>> water?
>>
>> Is it 300K at 1atm?
>>
>> thanks
>> sikandar
>>
>>  No. You have to equilibrate because the box is not completely full.
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] Charmm force field with gromacs

[Sai Pooja]

Hi,

I need to use charmm22 all atom force field with gromacs. What would be the
best way to do this?
a) Use perl scripts
b) Use a git version in which charmm is implemented

Pooja
-- 
Quaerendo Invenietis-Seek and you shall discover.
-- 
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Re: [gmx-users] Thermodynamic State of SPC/E bulk water, by genbox

[David van der Spoel]

On 2010-06-18 18.24, Sikandar Mashayak wrote:

Hi

When a bulk SPC/E water box(.gro) is created using the command "genbox
-cs spc216.gro -box 4.0 4.0 4.0", what is the thermodynamic condition of
water?

Is it 300K at 1atm?

thanks
sikandar


No. You have to equilibrate because the box is not completely full.

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] how small rcoulomb can be

[Gaurav Goel]

I will re-ask my question as it didn't come out right in previous
mail. Read below.

On Wed, Jun 16, 2010 at 6:11 PM, Mark Abraham  wrote:
>
>
> - Original Message -
> From: Gaurav Goel 
> Date: Thursday, June 17, 2010 5:21
> Subject: [gmx-users] how small rcoulomb can be
> To: Discussion list for GROMACS users 
>
>> For my NPT/NVT simulations I'm using a BKS potential for dispersion
>> interactions (VdWtype=USER)  which has a cut-off of 0.55
>> nm. I also
>> set rcoulomb=rlist=0.55 nm.
>>
>> My first question is regarding the choice of rcoulomb=0.55nm. Any
>> thoughts on whether this rcoulomb is large enough to ascertain that
>> real space electrostatics interactions are fairly small (in comparison
>> to total coulombic interactions)?
>
> That's around half the size of typical rcoulomb values used for PME, so
> you'll need to adjust ewald_rtol and fourier_spacing to a considerable
> degree in order that the electrostatics your PME model is comparably
> accurate. If this model has been used with PME in the past, then you will
> have some guidance in its literature (though GROMACS does not make it easy
> to choose beta directly). This will mean the reciprocal-space processors are
> doing lots more work than normal, and you'll want to set -npme to be half of
> -np, or maybe zero. Even so, your parallel scaling will be noticeably worse
> than normal PME.

Thanks for your reply Mark. Any thoughts on instead increasing
rcoulomb and rlist. Will that be more efficient and/or accurate rather
than trying to adjust ewald_rtol and fourier_spacing with a very short
rcoulomb? In literature I found that the optimal value people have
used for beta is, beta*L=10.

In my simulations, for rcoulomb=0.55, beta*L=15.52
rcoulomb=0.9, beta*L=   9.49
How can I obtain the magnitude of maximum wave vector (i.e., 'm' in
Eq. 4.159 of manual 4.0)?

I have a separate question in regards to (conserved) energy drift in a
NVT simulation.

I first equilibrated my system for 1 ns in NPT ensemble. Then, I
turned-off the pressure coupling, further equilibrated my system for 1
ns In NVT ensemble [N=2160, V=20.43 nm^3, T=4000K; rcoulomb=rlist=0.9,
rvdw=0.55, nstlist=5]. Then in a production run of 3.5ns I get
following energy drifts:
Statistics over 3549897 steps [ 1000. thru 4549.8960 ps ], 1 data sets
All averages are exact over 3549897 steps

Energy  Average   RMSD Fluct.  Drift  Tot-Drift
---
Conserved En.-3.65264e+06  1893673.102718.4782
  65595.7

i.e. drift=0.16 kT/ns.

If nstlist=10, drift= 0.5kT/ns

Should I worry about these drifts?

-Gaurav
>
> Mark
>
>> My second question is in regards to doing long (~15-100 ns) NVE
>> simulations. It appears using coulombtype=PME-Switch will be the best
>> option to accurately conserve energy. Any thoughts on how to choose
>> rcoulomb_switch and rcoulomb?
>>
>> Thanks,
>> Gaurav
>> --
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[gmx-users] pdb2gmx: c-terminal oxygens considered duplicate atoms

[jak137]

Hi,

There seem to be a problem with pdb2gmx's way of handling c-terminal oxygen 
atoms. As far as I understand in the case of G53a6 force field there are two 
(excluding [None]) choices:
[ COO- ] with oxygen atoms named 'O1' and 'O2'
[ COOH ] with oxygen atoms named 'O' and 'OT' (and hydrogen atom 'HT')
However, it is impossible to provide in a pdb input file coordinates for both 
of the oxygen atoms [if atoms are to be sorted]. It happens due to the fact 
that in both cases, both oxygen atom names are translated to just 'O' and than 
one of them is recognized as duplicate and gets removed. A new position is 
later assigned. On the other hand, if one disables automatic name translation 
by editing a local copy of xlateat.dat than the program fails with a fatal 
error like "Atom O1 in residue LYS 18 not found in rtp entry with 12 atoms 
while sorting atoms".

The atom name translating function rename_atoms() is called in read_pdball() 
called from main() before looping over chains. Than in the chain loop function 
sort_pdbatoms() which checks for atom names in residue data is called and than 
remove_duplicate_atoms() is called. Only later in this loop user is asked to 
choose termini types.

Consider for example a pdb file with the following content (named Ala2.pdb):

ATOM  1  O   ALA  1   -0.321  -1.578  -1.457  1.00  300.00
ATOM  2  C   ALA  1   0.399   -0.898  -0.728  1.00  300.00
ATOM  3  CA  ALA  1   1.921   -0.898  -0.728  1.00  300.00
ATOM  4  N   ALA  1   2.443   0.454   -0.728  1.00  300.00
ATOM  5  CB  ALA  1   2.387   -1.667  0.505   1.00  300.00
ATOM  6  OT  ALA  2   -3.422  0.890   -1.054  1.00  300.00
ATOM  7  C   ALA  2   -2.239  0.642   -0.823  1.00  300.00
ATOM  8  N   ALA  2   -0.132  0.037   0.274   1.00  300.00
ATOM  9  CA  ALA  2   -1.557  0.220   0.471   1.00  300.00
ATOM  10 O   ALA  2   -1.574  0.787   -1.873  1.00  300.00
ATOM  11 CB  ALA  2   -1.833  1.297   1.516   1.00  300.00
END

Process it with:

echo "0 1" | pdb2gmx -v -ff G53a6 -f Ala2.pdb -ter

Even though the initial structure is correct, the resulting conf.gro file has 
two nearly overlapping c-terminal oxygens - the distance is only 0.46 Ang. It 
should be fixed by minimization, but it would be better if all atom positions 
were conserved by pdb2gmx.

One last thing. I think it would be prudent to mention the role of xlateat.dat 
file in a manual section describing the program. I have learned about the very 
existence of the file after studying the sources... Only later I found a post 
from 2003 that gives an explanation: 
http://oldwww.gromacs.org/pipermail/gmx-users/2003-October/007378.html 

Best regards and thank you for a great program!

 jak


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[gmx-users] Thermodynamic State of SPC/E bulk water, by genbox

[Sikandar Mashayak]

Hi

When a bulk SPC/E water box(.gro) is created using the command "genbox -cs
spc216.gro -box 4.0 4.0 4.0", what is the thermodynamic condition of water?

Is it 300K at 1atm?

thanks
sikandar
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Re: [gmx-users] Plotting Energies versus time

[Justin A. Lemkul]

Rabab Toubar wrote:

Hi,

I want to extract the values for potential E, kinetic E, total E, and 
temperature from the log file so as to plot them versus time. In NAMD it is 
easy to do that using cat |grep, is there a similar way to do it in GMX



That's what g_energy is for.

-Justin


Thanks
Rabab Toubar



  



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Ph.D. Candidate
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Department of Biochemistry
Virginia Tech
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[gmx-users] charmm 22 all atom

[Sai Pooja]

Hi,

I need to use charmm22 all atom force field with gromacs. What would be the
best way to do this?
a) Use perl scripts
b) Use a git version in which charmm is implemented

Pooja

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[gmx-users] Plotting Energies versus time

[Rabab Toubar]

Hi,

I want to extract the values for potential E, kinetic E, total E, and 
temperature from the log file so as to plot them versus time. In NAMD it is 
easy to do that using cat |grep, is there a similar way to do it in GMX

Thanks
Rabab Toubar



  

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Re: [gmx-users] Incomplete ring

[Justin A. Lemkul]

you zou wrote:

Hi again,

Thank you, I added missing atoms with emacs, but my question is this ring
doesn't have to be complete and if I add missing atoms with HIS680's name, I
change its structure. Is it true?



All structures have to be complete in order for pdb2gmx to process them.  The 
only atoms it can add are hydrogens.  All heavy atoms are required.


If you place the missing atom(s) correctly, according to proper geometry, you 
shouldn't be changing the structure too much, but a simple energy minimization 
after you've generated the topology should relax any poor geometry.


-Justin




Hi Users,

I have a .pdb file, in this file when I want to use pdb2gmx command there
is this error massage: Fatal error: Incomplete ring in HIS680

this aminoacid is not complete in general, I don't know how can I complete
this such that I don't add HIS for complete? Please give me a hint.


add the missing atoms with emacs (or another text editor). Then minimize.

Thank you



 
Hotmail: Free, truste d and rich email service. Get it now. 





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MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Incomplete ring

[you zou]

Hi again,Thank you, I added missing atoms with emacs, but my question is this 
ring doesn't have to be complete and if I add missing atoms with HIS680's name, 
I change its structure. Is it true?
> Hi Users,
>
> I have a .pdb file, in this file when I want to use pdb2gmx command
> there is this error massage:
> Fatal error:
> Incomplete ring in HIS680
>
> this aminoacid is not complete in general, I don't know how can I
> complete this such that I don't add HIS for complete? Please give me a hint.
>
add the missing atoms with emacs (or another text editor). Then minimize.
> Thank you
  
_
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Re: [gmx-users] how small rcoulomb can be

[Gaurav Goel]

Thanks for your reply Mark.

On Wed, Jun 16, 2010 at 6:11 PM, Mark Abraham  wrote:
>
>
> - Original Message -
> From: Gaurav Goel 
> Date: Thursday, June 17, 2010 5:21
> Subject: [gmx-users] how small rcoulomb can be
> To: Discussion list for GROMACS users 
>
>> For my NPT/NVT simulations I'm using a BKS potential for dispersion
>> interactions (VdWtype=USER)  which has a cut-off of 0.55
>> nm. I also
>> set rcoulomb=rlist=0.55 nm.
>>
>> My first question is regarding the choice of rcoulomb=0.55nm. Any
>> thoughts on whether this rcoulomb is large enough to ascertain that
>> real space electrostatics interactions are fairly small (in comparison
>> to total coulombic interactions)?
>
> That's around half the size of typical rcoulomb values used for PME, so
> you'll need to adjust ewald_rtol and fourier_spacing to a considerable
> degree in order that the electrostatics your PME model is comparably
> accurate. If this model has been used with PME in the past, then you will
> have some guidance in its literature (though GROMACS does not make it easy
> to choose beta directly). This will mean the reciprocal-space processors are
> doing lots more work than normal, and you'll want to set -npme to be half of
> -np, or maybe zero. Even so, your parallel scaling will be noticeably worse
> than normal PME.

Thanks for your reply Mark. Any thoughts on instead increasing
rcoulomb and rlist. Will that be more efficient and/or accurate rather
than trying to adjust ewald_rtol and fourier_spacing with a very short
rcoulomb? In literature I found that the optimal value people have
used for beta is, beta*L=10.

In my simulations, for rcoulomb=0.55, beta*L=15.52
 rcoulomb=0.9, beta*L=   9.49
How can I obtain the magnitude of maximum wave vector (i.e., 'm' in
Eq. 4.159 of manual 4.0)?

I have a separate question in regards to (conserved) energy drift in a
NVT simulation.

I first equilibrated my system for 1 ns in NPT ensemble. Then, I
turned-off the pressure coupling, further equilibrated my system for 1
ns In NVT ensemble [N=2160, V=20.43 nm^3, T=4000K; rcoulomb=rlist=0.9,
rvdw=0.55, nstlist=5]. Then in a production run of 3.5ns I get
following energy drifts:
Statistics over 3549897 steps [ 1000. thru 4549.8960 ps ], 1 data sets
All averages are exact over 3549897 steps

Energy  Average   RMSD Fluct.  Drift  Tot-Drift
---
Conserved En.-3.65264e+06  1893673.102718.4782
   65595.7

i.e. drift=0.16 kT/ns.

If nstlist=10, drift= 0.5kT/ns

Should I worry about these drifts?

-Gaurav

>
> Mark
>
>> My second question is in regards to doing long (~15-100 ns) NVE
>> simulations. It appears using coulombtype=PME-Switch will be the best
>> option to accurately conserve energy. Any thoughts on how to choose
>> rcoulomb_switch and rcoulomb?
>>
>> Thanks,
>> Gaurav
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Re: [gmx-users] a query about analysis

[Mark Abraham]

- Original Message -
From: oguz gurbulak 
Date: Friday, June 18, 2010 21:36
Subject: [gmx-users] a query about analysis
To: gmx-users@gromacs.org

---
|  -  -  - > Dear All, 

  I study on molecular dynamics simulations of organic molecules. I want to 
learn that Is there an excel-like program that accepts more data set ( for 
instance output info for 5000 records ) in order to make analysis ? Could you 
please give me some suggestions about this issue ?

 
 |
---
Excel is best at a small number of fixed data sets, or where you have the 
resources to build some kind of automated import mechanism and the capacity to 
program custom analysis functions as required. However running some magic macro 
to import and analyze your data simply doesn't scale to 5000 data sets. Were 
you to go to all that trouble, you may as well use a tool more suited to the 
task. Serious numerical work is more often done in R, S, SPSS, Matlab or such, 
simply because Excel is a generic tool and will not be able to support all 
specialized needs. Excel's default plot formats are particularly unsuited to 
scientific needs.

GROMACS provides a large number of command-line tools, which can do most tasks 
most users want to do. Learning to write simple shell scripts to loop over 
whatever is creating your 5000 records is a very worthwhile investment for 
future running and analysis of calculations. gnuplot or xmgrace are desirable 
plotting tools in this context, though you should check the GROMACS wiki for 
more suggestions.

Mark

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Re: [gmx-users] a query about analysis

[shayamra]

There are many programs you could use for large data sets, although  
I'm not sure how many of them belong to the "excel-like" category.


Personally, I'm quite happy with Matlab and its free-counterpart,  
Octave. Both of them can quite easily be made to read matrices and  
xvg-files. They are much faster too (in terms of generating plots,  
etc.).
Using any of them is not strictely intuitive so you might have to hit  
some manuals in order to master them correctly.


Good luck,
-Shay

Quoting "oguz gurbulak" :






Dear All,

 

I study on molecular dynamics simulations of organic molecules. I want to
learn that Is there an
excel-like program that accepts more data set ( for instance output  
info for 5000
records ) in order to make analysis ? Could you please give me some  
suggestions about this issue ?


 

Thank you very much for your attention.

 

Kind regards.










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Re: [gmx-users] a query about analysis

[Erik Marklund]

oguz gurbulak skrev:


Dear All,

 

I study on molecular dynamics simulations of organic molecules. I want 
to learn that Is there an excel-like program that accepts more data 
set ( for instance output info for 5000 records ) in order to make 
analysis ? Could you please give me some suggestions about this issue ?


 


Thank you very much for your attention.

 


Kind regards.



Hi,

It's a bit unclear to me exactly what you mean, but no, there is no 
excel-like program that I know of if it's the spreadsheet style that 
you're after. xmgrace accepts multiple data sets, and creative scripting 
can be used to call the gromacs analysis tools 5000 times.


--
---
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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[gmx-users] a query about analysis

[oguz gurbulak]

Dear All, 

  

I study on molecular dynamics simulations of organic molecules. I want to
learn that Is there an
excel-like program that accepts more data set ( for instance output info for 
5000
records ) in order to make analysis ? Could you please give me some suggestions 
about this issue ? 

  

Thank you very much for your attention. 

  

Kind regards.






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Re: [gmx-users] Re: His protonation

[Justin A. Lemkul]

Tsjerk Wassenaar wrote:

There are no protons in crystal structures.


http://www.rcsb.org/pdb/explore/explore.do?structureId=2VB1



I stand corrected :)  In general, though, most crystal structures do not have 
resolution sufficient enough to assign hydrogen positions.  This one is 
especially good!


-Justin

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Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
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Re: [gmx-users] Question about topologies

[Erik Marklund]

Thanasis Koukoulas skrev:

Hello

[ atomtypes ]
; type mass charge ptype c6 c12
CH3 15.035 0.000 A 9.0638e-3 2.5206e-5
CH2 14.027 0.000 A 5.8108e-3 2.2071e-5
CS2 14.027 0.000 A 5.8108e-3 2.2071e-5
OS 15.999 0.000 A 8.8147e-4 4.2477e-7
OA 15.999 0.000 A 2.3465e-3 1.7802e-6
HO 1.008 0.000 A 0.e00 0.e00

at atomtypes i can give c6 and c12 values and gromacs will generate 
the c6ij and c12ij values from the formulas i have chosen with 
selecting combination rule Am i right


in my case i gave c6 and c12 as c6i=4*ei*σi^6 and c12i=4*ei*σi^12 and 
i chose combination rule 1. so gromacs will generate the c6ij and 
c12ij as c6ij=sqrt(C6iC6j) and c12ij=sqrt(c6i*c12j)


So if in my topology I put [nonbond_params] what happens then? the 
values from [nonbond_params] c6 and c12 are being replaced by the 
values gromacs finds from the equations???


for example

if i have

[nonbond_params]

CH3 CH3 5e-3 6e-5

and gromacs calculates from the [atomtypes] are different lets say (i 
didnt do the calculation it is an assumption value) 3e-2 and 3e-5 
which values gromacs accepts?

i have read the manual but it isnd clear how this works.

please someone enlighten me.

thanks



HI,

One good way of finding out is to generate two tpr-files and compare 
them with the help of gmxdump.


--
---
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Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] Question about topologies

[Mark Abraham]

- Original Message -
From: Thanasis Koukoulas 
Date: Friday, June 18, 2010 19:55
Subject: [gmx-users] Question about topologies
To: gmx-users@gromacs.org

---
| > Hello
> [ atomtypes ]> ;   type  masschargeptype   c6c12> 
> CH3 15.035 0.000A   9.0638e-3  2.5206e-5> CH2 
> 14.027 0.000A   5.8108e-3  2.2071e-5> CS2 14.027 
> 0.000A   5.8108e-3  2.2071e-5> OS  15.999 0.000A  
>  8.8147e-4  4.2477e-7 > OA  15.999  0.000A   
> 2.3465e-3  1.7802e-6> HO   1.008 0.000A   0.e00   
>0.e00 > 
> at atomtypes i can give c6 and c12 values and gromacs will generate the c6ij 
> and c12ij values from the formulas i have chosen with selecting combination 
> rule Am i right> 
> in my case i gave c6 and c12 as c6i=4*ei*σi^6 and c12i=4*ei*σi^12 and i chose 
> combination rule 1. so gromacs will generate the c6ij and c12ij as 
> c6ij=sqrt(C6iC6j) and c12ij=sqrt(c6i*c12j)> 
> So if in my topology I put [nonbond_params] what happens then? the values 
> from [nonbond_params] c6 and c12 are being replaced by the values gromacs 
> finds from the  equations???> 
> for example> 
> if i have > 
> [nonbond_params] > 
> CH3 CH3 5e-3 6e-5> 
> and gromacs calculates from the [atomtypes] are different lets say (i didnt 
> do the calculation it is an assumption  value) 3e-2 and 3e-5 which values 
> gromacs accepts?> i have read the manual but it isnd clear how this works.

Manual 5.3.3 covers this.

Mark
 |
---

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[gmx-users] Question about topologies

[Thanasis Koukoulas]

Hello
[ atomtypes ];   type      mass    charge    ptype       c6            c12    
CH3     15.035     0.000    A       9.0638e-3      2.5206e-5    CH2     14.027  
   0.000    A       5.8108e-3      2.2071e-5    CS2     14.027     0.000    A   
    5.8108e-3      2.2071e-5    OS      15.999     0.000    A       8.8147e-4   
   4.2477e-7     OA      15.999     0.000    A       2.3465e-3      1.7802e-6   
 HO       1.008     0.000    A       0.e00      0.e00 
at atomtypes i can give c6 and c12 values and gromacs will generate the c6ij 
and c12ij values from the formulas i have chosen with selecting combination 
rule Am i right
in my case i gave c6 and c12 as c6i=4*ei*σi^6 and c12i=4*ei*σi^12 and i chose 
combination rule 1. so gromacs will generate the c6ij and c12ij as 
c6ij=sqrt(C6iC6j) and c12ij=sqrt(c6i*c12j)
So if in my topology I put [nonbond_params] what happens then? the values 
from [nonbond_params] c6 and c12 are being replaced by the values gromacs finds 
from the equations???
for example
if i have 
[nonbond_params] 
CH3 CH3 5e-3 6e-5
and gromacs calculates from the [atomtypes] are different lets say (i didnt do 
the calculation it is an assumption  value) 3e-2 and 3e-5 which values gromacs 
accepts?i have read the manual but it isnd clear how this works. 
please someone enlighten me.
thanks

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RE: [gmx-users] constraints bond length vari by 10%

[Berk Hess]

Hi,

shake_tol sets the relative tolerance of the constraint lengths.
This means that the constraints should not differ more than +-shake_tol
after constraining: for example a constraint of length 0.1 nm with 
shake_tol=1e-4
should be between 0.0 and 0.10001 nm.

Note that the settings in your last mail are quite close to the floating point 
precision.
Double precision could help in that case.
But your earlier mails also seem to indicate problems with lower shake_tols.
I have no clue what could be wrong in that case.

BTW have you tried LINCS?

Berk

> From: sebastian.wa...@physik.uni-freiburg.de
> Subject: Re: [gmx-users] constraints bond length vari by 10%
> To: gmx-users@gromacs.org
> Date: Fri, 18 Jun 2010 09:20:05 +0200
> 
> I don't who does not get it right. My constraints work and
> it does change when I comment out the constraints. I put
> the constraints right there they write it in the
> Documentation. I do not even include water.itp. My question
> is how I can constrain the bonds more rigid. And for this I
> would like to know what does the shake_tol means. 
> 
> Thanks
> 
> 
> On Fri, 18 Jun 2010 09:37:36 +1000
>  Mark Abraham  wrote:
> > 
> > 
> > - Original Message -
> > From: Sebastian Waltz
> > 
> > Date: Thursday, June 17, 2010 18:59
> > Subject: Re: [gmx-users] constraints bond length vari by
> > 10%
> > To: Discussion list for GROMACS users
> > 
> > 
> > > Hi,
> > > 
> > > I did read the Documentation 5 times now, but I still
> > not
> > > get is what the shake_tol does tell me. I tried it with
> > 10
> > > values and can't figure out what it does. My CO bonds
> > are
> > > constraint. Otherwise I would have bigger variations of
> > the
> > > bond length. My .mdp file looks like this
> > > 
> > > constraints = none
> > > constraint_algorithm= shake
> > > shake_tol   = 0.05
> > > unconstrained_start = no
> > > 
> > > My question is more how I can constrain the bond length
> > > such that they vary only by a factor of +/- 0.0001. 
> > 
> > The above is fine, except that your topology probably has
> > no constraints defined in it, because your [constraints]
> > is in the wrong place. Try commenting out the contents of
> > your constraints directive and see if you get identical
> > results. This is the last time I'm going to repeat
> > myself, since you're appearing to ignore my feedback :-)
> > 
> > Mark
> > 
> > > On Thu, 17 Jun 2010 08:01:04 +1000
> > >  Mark Abraham  wrote:
> > > > 
> > > > 
> > > > - Original Message -
> > > > From: Sebastian Waltz
> > > > 
> > > > Date: Thursday, June 17, 2010 2:23
> > > > Subject: Re: [gmx-users] constraints bond length vari
> > by
> > > > 10%
> > > > To: Discussion list for GROMACS users
> > > > 
> > > > 
> > > > > Hi Mark,
> > > > > 
> > > > > what I have written in the .top you can see in my
> > first
> > > > > massage. 
> > > > 
> > > > OK - but my suggestion was that it was put in the
> > wrong
> > > > *place* and I don't have enough information to say
> > > > whether that's true.
> > > > 
> > > > > I actually don't know what to write what and in
> > > > > which .itp/.tpr file I have to add something and I
> > also
> > > > > can't find something in the Internet. The
> > documentation
> > > > for
> > > > > the constraints is just bad.
> > > > 
> > > > I understand your frustration, but documentation
> > can't
> > > > anticipate the answer to every question or it would
> > be
> > > > infinitely long. That fact doesn't make it bad. What
> > the
> > > > documentation can do is provide general instruction.
> > If
> > > > my guess is correct, then the worked example of a
> > .top
> > > > file in Chapter 5 will help you understand where
> > > > [constraints] needs to go. Specifically, page 109
> > will
> > > > point out that
> > > > 
> > > > #include "ffforcefield.itp"
> > > > [ moleculetype ]
> > > > ...
> > > > [atoms]
> > > > ...
> > > > 
> > > > #include "water.itp"
> > > > 
> > > > [system]
> > > > ...
> > > > [molecules]
> > > > ...
> > > > 
> > > > [constraints]
> > > > ...
> > > > 
> > > > won't work.
> > > > 
> > > > Section 5.5 has a worked example of how to use
> > [settles]
> > > > which are a kind of constraint, and work the same
> > way.
> > > > 
> > > > Once you've worked through this information, if you
> > still
> > > > have a problem with the documention, then a
> > constructive
> > > > suggestion for improvement would be welcome :-)
> > > > 
> > > > Mark
> > > > 
> > > > > On Wed, 16 Jun 2010 09:05:20 +1000
> > > > >  Mark Abraham  wrote:
> > > > > > 
> > > > > > 
> > > > > > - Original Message -
> > > > > > From: Sebastian Waltz
> > > > > > 
> > > > > > Date: Tuesday, June 15, 2010 22:09
> > > > > > Subject: [gmx-users] constraints bond length vari
> > by
> > > > 10%
> > > > > > To: gmx-users@gromacs.org
> > > > > > 
> > > > > > > Hi all,
> > > > > > > 
> > > > > > > I added constraints on some bonds in my system
> > by
> > > > > > adding 
> > > > > > > 
> > > > > > > [ constraints ]
>

[gmx-users] Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76

[Carsten Kutzner]

Hi Abdul,

please keep Gromacs-related questions on the list. The error
is exactly as printed: You have more than 128 backups of md.log
in your directory, at this point mdrun does not make more backups
of md.log any more. You have to delete the #md.log.*# files.

Carsten


On Jun 18, 2010, at 7:24 AM, abdul wadood wrote:

> Dear Carsten
> 
> When I reduce the number of steps in mdp file the error change which now
> 
> 0: Fatal error:
> 0: Won't make more than 128 backups of md.log for you
> 0: ---
> 0:
> 0: "I Wonder, Should I Get Up..." (J0: p0_27074:  p4_error: : -1
> . Lennon)
> 0:
> 0: Halting program mdrun_mpi
> 0:
> 0: gcq#46: "I Wonder, Should I Get Up..." (J. Lennon)
> 0:
> 0: [0] MPI Abort by user Aborting program !
> 0: [0] Aborting program!
> 0: p4_error: latest msg from perror: No such file or directory
> 
> 
> Abdul Wadood, 
> Research Scholar, 
> Dr.Panjwani Center for Molecular Medicine and 
> Drug Research, 
> International Center for Chemical and 
> Biological Science, 
> University of Karachi, Karachi-75720, Pakistan. 
> Email:wadoodbiochem...@hotmail.com 
> 
> 
> 
> 
> From: ckut...@gwdg.de
> Subject: Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76
> Date: Thu, 17 Jun 2010 16:36:51 +0200
> To: wadoodbiochem...@hotmail.com
> 
> On Jun 17, 2010, at 3:57 PM, abdul wadood wrote:
> 
> Dear Carsten
> 
> I give the path for the topol.tpr file now the error is change which is
> 
> Fatal error:
> 3: Too many LINCS warnings (4254)
> 3: If you know what you are doing you can adjust the lincs warning threshold 
> in your mdp file
> 3: or set the environment variable GMX_MAXCONSTRWARN to -1,
> 3: but normally it is better to fix the problem
> 3: ---
> 3:
> Maybe your system is not well equilibrated, or your time step is too long.
> 
> Carsten
> 
> Hotmail is redefining busy with tools for the New Busy. Get more from your 
> inbox. See how.


--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne




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Re: [gmx-users] constraints bond length vari by 10%

[Sebastian Waltz]

I don't who does not get it right. My constraints work and
it does change when I comment out the constraints. I put
the constraints right there they write it in the
Documentation. I do not even include water.itp. My question
is how I can constrain the bonds more rigid. And for this I
would like to know what does the shake_tol means. 

Thanks


On Fri, 18 Jun 2010 09:37:36 +1000
 Mark Abraham  wrote:
> 
> 
> - Original Message -
> From: Sebastian Waltz
> 
> Date: Thursday, June 17, 2010 18:59
> Subject: Re: [gmx-users] constraints bond length vari by
> 10%
> To: Discussion list for GROMACS users
> 
> 
> > Hi,
> > 
> > I did read the Documentation 5 times now, but I still
> not
> > get is what the shake_tol does tell me. I tried it with
> 10
> > values and can't figure out what it does. My CO bonds
> are
> > constraint. Otherwise I would have bigger variations of
> the
> > bond length. My .mdp file looks like this
> > 
> > constraints = none
> > constraint_algorithm= shake
> > shake_tol   = 0.05
> > unconstrained_start = no
> > 
> > My question is more how I can constrain the bond length
> > such that they vary only by a factor of +/- 0.0001. 
> 
> The above is fine, except that your topology probably has
> no constraints defined in it, because your [constraints]
> is in the wrong place. Try commenting out the contents of
> your constraints directive and see if you get identical
> results. This is the last time I'm going to repeat
> myself, since you're appearing to ignore my feedback :-)
> 
> Mark
> 
> > On Thu, 17 Jun 2010 08:01:04 +1000
> >  Mark Abraham  wrote:
> > > 
> > > 
> > > - Original Message -
> > > From: Sebastian Waltz
> > > 
> > > Date: Thursday, June 17, 2010 2:23
> > > Subject: Re: [gmx-users] constraints bond length vari
> by
> > > 10%
> > > To: Discussion list for GROMACS users
> > > 
> > > 
> > > > Hi Mark,
> > > > 
> > > > what I have written in the .top you can see in my
> first
> > > > massage. 
> > > 
> > > OK - but my suggestion was that it was put in the
> wrong
> > > *place* and I don't have enough information to say
> > > whether that's true.
> > > 
> > > > I actually don't know what to write what and in
> > > > which .itp/.tpr file I have to add something and I
> also
> > > > can't find something in the Internet. The
> documentation
> > > for
> > > > the constraints is just bad.
> > > 
> > > I understand your frustration, but documentation
> can't
> > > anticipate the answer to every question or it would
> be
> > > infinitely long. That fact doesn't make it bad. What
> the
> > > documentation can do is provide general instruction.
> If
> > > my guess is correct, then the worked example of a
> .top
> > > file in Chapter 5 will help you understand where
> > > [constraints] needs to go. Specifically, page 109
> will
> > > point out that
> > > 
> > > #include "ffforcefield.itp"
> > > [ moleculetype ]
> > > ...
> > > [atoms]
> > > ...
> > > 
> > > #include "water.itp"
> > > 
> > > [system]
> > > ...
> > > [molecules]
> > > ...
> > > 
> > > [constraints]
> > > ...
> > > 
> > > won't work.
> > > 
> > > Section 5.5 has a worked example of how to use
> [settles]
> > > which are a kind of constraint, and work the same
> way.
> > > 
> > > Once you've worked through this information, if you
> still
> > > have a problem with the documention, then a
> constructive
> > > suggestion for improvement would be welcome :-)
> > > 
> > > Mark
> > > 
> > > > On Wed, 16 Jun 2010 09:05:20 +1000
> > > >  Mark Abraham  wrote:
> > > > > 
> > > > > 
> > > > > - Original Message -
> > > > > From: Sebastian Waltz
> > > > > 
> > > > > Date: Tuesday, June 15, 2010 22:09
> > > > > Subject: [gmx-users] constraints bond length vari
> by
> > > 10%
> > > > > To: gmx-users@gromacs.org
> > > > > 
> > > > > > Hi all,
> > > > > > 
> > > > > > I added constraints on some bonds in my system
> by
> > > > > adding 
> > > > > > 
> > > > > > [ constraints ]
> > > > > > ;ai aj  typedistance
> > > > > >40   41  1   0.1230
> > > > > >47   48  1   0.1230
> > > > > >54   55  1   0.1230
> > > > > >61   62  1   0.1230
> > > > > > 
> > > > > > to me top file (CO double bonds) and in the mdp
> > > file 
> > > > > > 
> > > > > > 
> > constraints 
> > > > > > =  none
> > > > > > 
> > > > > > . I thought this should more or less fix my
> bond
> > > > > lengths.
> > > > > > Nether the less the bond lengths vary by 10%.
> Did I
> > > > > make
> > > > > > something or is it quite normal? What would be
> the
> > > way
> > > > > to
> > > > > > fix the bond length so that they vary only by
> ca.
> > > 1%.
> > > > > 
> > > > > You're using the right approach, but you've
> probably
> > > not
> > > > > put your [constraints] directive in the right
> > > > > [moleculetype], or used the wrong .top/.itp/.tpr
> file
> > > at
> > > > > some point.
> > > > > 
> > > > > Mark
> > > > > 
> > > > 
> > > > -- 
> > > > gmx-users 

Re: [gmx-users] Re: His protonation

[Tsjerk Wassenaar]

> There are no protons in crystal structures.

http://www.rcsb.org/pdb/explore/explore.do?structureId=2VB1

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
-- 
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