Re: [gmx-users] GROMACS on CYGWIN

[Vasilii Artyukhov]

Also, use the 'nice' command to run gmx at high priority, and switch off CPU
frequency scaling. For me, cygwin performance is pretty much the same as
that on linux, which is to be expected since most of the code isn't
dependent on system calls. Apparently, the only difference you should be
able to see is in disk I/O, but you don't want to I/O too frequently anyway.

On Fri, Jun 11, 2010 at 3:18 AM, Mark Abraham wrote:

>
>
> - Original Message -
> From: Nasim Biglari 
> Date: Friday, June 11, 2010 2:51
> Subject: [gmx-users] GROMACS on CYGWIN
> To: gmx-users@gromacs.org
>
> > Dear all,
> >
> > I was wondering whether GROMACS on CYGWIN is less capable than GROMACS
> run on LINUX?
> >  i.e. concerning its speed and its ability to simulate larger
> macromolecules. I assume that it is faster, but is it very much different?
>
> GROMACS will run fine, and do approximately the same under either OS on
> comparable hardware with the same version of gcc, however for production
> simulation to be maximally effective you need to arrange for the simulation
> process not to be interrupted much. This is easier to arrange on Linux than
> Windows. You certainly don't want to be concurrently using either kind of
> machine as a desktop, and also you'd prefer not to be logged on to either
> machine.
>
> Mark
>
>
> --
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Re: [gmx-users] error in hydrocarbon dihedrals of opls-aa?

[Vasilii Artyukhov]

Dear Markus,

Just a follow-up: how did it all end, were able to find the source of error
(if any)?

2010/5/10 Markus Tusch 

> Am 07.05.2010 16:03, schrieb David van der Spoel:
>
>  On 5/7/10 8:45 AM, Markus Tusch wrote:
>>
>>> Hi everybody,
>>>
>>> I've just compared the following opls-aa torsional parameters for
>>> hydrocarbons given in J. Comp. Chem., Vol. 18, No. 16, 1955 - 1970 (1997)
>>> as well as in J. Comp. Chem., Vol. 23, No. 15, 1416 - 1429 (2002)
>>> with those in ffoplsaabon.itp (Gromacs 4.0.7):
>>>
>>> ##literature (these are also the original values for alkanes published
>>> by Jorgensen in 1996 I believe):
>>> V1 V2 V3
>>> H-C-C-H 0.0 0.0 0.318
>>> H-C-C-C 0.0 0.0 0.366
>>> C-C-C-C 1.74 -0.157 0.279
>>>
>>> ##ffoplsaabon.itp, keyword "hydrocarbon", (translated according to eq.
>>> 4.64 of the manual):
>>>
>>> V1 V2 V3
>>> H-C-C-H 0.0 0.0 0.300
>>> H-C-C-C 0.0 0.0 0.300
>>> C-C-C-C 1.299 -0.05 0.200
>>>
>>> There's obviously a difference.
>>> Is there another source for the latter parameters which I just wasn't
>>> able to find? I know that the numbers in Gromacs were updated in 1999.
>>>
>>> Cheers,
>>> Markus
>>>
>>>  Hi Markus,
>>
>> Erik Lindahl made those conversions based on a file provided by Jorgensen.
>> This did not make it into gromacs before 3.1 which was well after 1999, but
>> there was a downloadable force field earlier.
>>
>> Now the question is whether
>> - the OPLS force field changed after 1996 when this was published
>> - Erik made an error when converting to Ryckaert Bellemans
>> - You made an error when converting back :).
>>
> Hi David,
> thanks for your reply.
>
> Well, for all the other 10 dihedrals (alcohols, ethers, acetals,
> carbohydrates) in the reference from 1997 (see above) my results match :).
> It's just the three hydrocarbon related ones that were significantly off.
> So I guess it's likely that exactly these parameters were changed at some
> point in between, although van Gunsteren still used them in 2002 (see
> above).
>
>
>
>> Looking at the ffoplsaabon.itp file I can not but notice that there are
>> more than 1 H C C C dihedrals which are all different:
>> C   CT CT   HC 3 -0.20934 -0.62802 0.0 0.83736 0.0 0.0 ;
>> C   CT CT_2 HC 3 -0.15910 -0.47730 0.0 0.63639 0.0 0.0
>> C_3 CT CT_2 HC 3 -0.15910 -0.47730 0.0 0.63639 0.0 0.0
>>
>> Neither of which seems to be consistent with the Eqn 4.64
>> Based on H-C-C-C 0.0 0.0 0.300 I would expect
>> H C C C 3 0.6276 1.8828 0 -1.2552 0
>>
>
> The one I am talking about is
> CT CT CT HC  3  0.62760   1.88280   0.0  -2.51040
> 0.0   0.0 ; hydrocarbon all-atom
> which was also used for
> CO CT CT HC  3  0.62760   1.88280   0.0  -2.51040
> 0.0   0.0 ; acetal
> and
> CT CT CO HC  3  0.62760   1.88280   0.0  -2.51040
> 0.0   0.0 ; acetal
> amongst others ...
>
> Except for the factor 2 in C3 these are very much consistent with your
> result, so maybe you just missed the 2 in C3 = -2 F3 in Eqn 4.64?
>
>
>> So I am lost here...
>>
>>
>
> --
> Markus Tusch M.Sc.
> University of Paderborn
> Faculty of Science
> Department of Chemistry
> Warburger Str. 100
> D-33098 Paderborn
> Germany
>
> Tel. +49-5251-60-5754
> e-mail mtu...@mail.upb.de
>
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[gmx-users] NPE simulations: where does all the energy go?

[Vasilii Artyukhov]

Dear colleagues,

There is probably some stupidity involved in my question, but I want to use
GROMACS to explore water phase equilibria using the phase coexistence
technique. This means that my simulation cell contains a liquid slab and an
ice slab in contact, and what I'm trying to do is to see which way the
interface moves depending on the external conditions. The system is
preequilibrated (100-ps NPT run at T slightly above or below the phase
transition temperature).

Now, normally one would want to use NVE simulations to just let the system
reach its equilibrium temperature, however, the density difference between
the liquid and the solid would result in all kinds of issues with pressure.
So it seems that a barostat is required. But what I see in NPE runs is that
my system loses energy. The total energy decreases perfectly linearly, with
both the potential energy and the temperature going down with time. I do
realize that my choice of subject to study might be rather unlucky in this
respect: since liquid water is more dense than ice, my system expands as its
energy decreases (freezing), and it also loses energy as it expands due to
mechanical work. As I understand it, some of this work might become lost
when using the first-order Berendsen barostat; however, what I would expect
from the Parrinello-Rahman barostat is to store this work in the barostat's
own "kinetic energy". And in the PR  case, the temperature drop/total energy
loss is indeed slower, but it's still there. Anyway, the temperature is
supposed to remain constant in this process, but it doesn't.

At this point I should probably mention that I'm using cutoffs for
intermolecular interactions with PME and the long-range dispersion
correction, and not PME-Switch/shifted which are advised for constant-energy
runs; however, I don't really believe that cutoff issues could explain an
effect that strong.

Sorry for the probably cumbersome explanations, but it seems I really need
some help from someone more experienced with NPE simulations to figure
out *where
does all my energy go*. Could there be some algorithmic caveat I'm unaware
of, or perhaps this behavior is completely natural and I'm just missing some
simple basic physics?

Thanks in advance,
Vasilii
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Re: [gmx-users] visualization tool for windows

[Vasilii Artyukhov]

Have you tried loading the .gro into VMD first? VMD requires it to
understand the contents of your trr/xtc files. I believe that VMD can
sometimes find it automatically, but sometimes it can't, and you have to
first load it and then load the trajectory.
Otherwise, you can trjconv your trajectory to .pdb or .gro (mind that the
resulting files are going to be huge and the precision of coordinates and
velocities will suffer strongly).

2009/9/22 

> Hello,
> Is there a visualization tool to see .trr files on a windows machine?
> I already have VMD, but the windows version does not seem to play
> trajectory files.
> Thanks
> Alberto
>
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Re: [gmx-users] Gromacs using MKL with Intel 11.1 compilers

[Vasilii Artyukhov]

Hi,


> Anybody have any real-world comparisons of using MKL vs. FFTW3?
>

http://www.quantumespresso.org/user_guide/node16.html says:

Axel Kohlmeyer suggests the following (April 2008): "(I've) found that Intel
is now turning on multithreading without any warning and that is for example
why their FFT seems faster than FFTW. For serial and OpenMP based runs this
makes no difference (in fact the multi-threaded FFT helps), but if you run
MPI locally, you actually lose performance. Also if you use the 'numactl'
tool on linux to bind a job to a specific cpu core, MKL will still try to
use all available cores (and slow down badly). The cleanest way of avoiding
this mess is to either link with

-lmkl_intel_lp64 -lmkl_sequential -lmkl_core (on 64-bit: x86_64, ia64)
-lmkl_intel -lmkl_sequential -lmkl_core (on 32-bit, i.e. ia32 )

or edit the libmkl_'platform'.a file (I'm using now a file libmkl10.a with:

  GROUP (libmkl_intel_lp64.a libmkl_sequential.a libmkl_core.a)

It works like a charm".

So, this might contribute to your problem. Please tell us if Axel's
suggestion works for you!

Best regards,
Vasilii
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[gmx-users] Regarding the 'hangs at "atom 0"' issue with x2top 4.x

[Vasilii Artyukhov]

Hi all,

I've recently managed to reproduce the bug with x2top 4.x hanging at "atom
0". The halt occurred when I was trying to generate a topology with the
"-pbc yes" option (which is the default used unless you specify otherwise)
using a structure file containing no information on the periodic box. As
soon as I added the box info, x2top 4.0.4 did successfully generate a
topology for me.

I'm using x2top for periodic molecules (just forgot to add the box string
this one time), so I didn't bother actually trying to turn off PBC, but I
strongly suspect that this is the actual source of the problem reported by
many colleagues on the list. Perhaps someone who previously complained about
x2top 4.x halting should try first adding the -nopbc option to their command
line and then adding the box vectors to their .gro and tell us all what
happens then! :) Also, the developers might want to consider doing something
about this setting and its default value.

Aside from this one time, I've never had any problems with x2top 4.0.4
(especially with the -noparam option that I use all the time, just to keep
things simple), and its value at generating topologies for my 2D periodic
molecules cannot be overemphasized :)

Hope this helps someone,
Vasilii
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Re: [gmx-users] Re: CNT

[Vasilii Artyukhov]

Hmm... I've been using the 4.0.4 x2top to create OPLS-AA topologies for,
e.g., graphane, and it worked more or less right "out of the box", giving
very convincing results. What's the problem exactly about recent versions of
x2top? I use the -noparams option to leave everything having to do with
numbers to grompp. Even periodic boundary conditions for infinite molecules
seem to be handled correctly...

2009/7/30 Vitaly V. Chaban 

> Giulio,
>
> I suggest you to try x2top which is spread with gromacs-3.3.1. The
> newer versions of x2top are not sain.
>
> Vitaly
>
> On Thu, Jul 30, 2009 at 1:48 PM, Giulio Scocchi
> wrote:
> > Hi Vitaly
> >
> > Well, I have downloaded it just a couple of months ago, so I guess it
> should be 4.0.4
> >
> > Giulio
> >
> >
> 
> >
> > Giulio Scocchi
> >
> > iCIMSI - Institute of Computer Integrated Manufacturing for Sustainable
> Innovation
> > www.icimsi.ch
> > DTI - Department of Innovative Technologies
> > www.dti.supsi.ch
> > SUPSI - University of Applied Science of Southern Switzerland
> > www.supsi.ch
> >
> > Via Cantonale - Galleria 2
> > 6928 Manno
> > Switzerland
> > tel: +41 (0)58 666 66 46
> > fax: +41 (0)58 666 66 20
> >
> >
> > -Messaggio originale-
> > Da: Vitaly V. Chaban [mailto:vvcha...@gmail.com]
> > Inviato: giovedì, 30. luglio 2009 12:42
> > A: gmx-users@gromacs.org
> > Cc: Giulio Scocchi
> > Oggetto: Re: CNT
> >
> > Hi,
> >
> > What's the version of your gromacs?
> >
> > ~ Vitaly
> >
> >>
> >> I am a Gromacs beginner and I am trying to simulate an infinite graphene
> >> lattice (see 07.29.09 posts - I don't know how to reply directly to
> >> posts, can someone tell me how to do that?). Mark suggested having a
> >> look at  http://www.gromacs.org/WIKI-import/Carbon_Nanotube . I had
> >> already seen that and I hoped there were some kind of more "direct" way.
> >> Anyway, I tried to follow the procedure explained  in Christopher Stiles
> >> website (http://cs86.com/CNSE/SWNT.htm) just to simulate the nanotube
> >> (graphene will come). I downloaded all the files and (as it was
> >> suggested) typed:
> >>
> >>
> >>
> >>  x2top -f SWNT_6_6_144.pdb -o SWNT_6_6_144.top -r SWNT_6_6_144.rtp
> >>
> >>
> >>
> >> and this is what happened:
> >>
> >>
> >>
> >> Opening library file
> >> /homea/scocchi/GROMACS/share/gromacs/top/aminoacids.dat
> >>
> >> WARNING: masses will be determined based on residue and atom names,
> >>
> >> this can deviate from the real mass of the atom type
> >>
> >> Opening library file
> >> /homea/scocchi/GROMACS/share/gromacs/top/atommass.dat
> >>
> >> Entries in atommass.dat: 178
> >>
> >> WARNING: vdwradii will be determined based on residue and atom names,
> >>
> >> this can deviate from the real mass of the atom type
> >>
> >> Opening library file
> >> /homea/scocchi/GROMACS/share/gromacs/top/vdwradii.dat
> >>
> >> Entries in vdwradii.dat: 28
> >>
> >> Opening library file /homea/scocchi/GROMACS/share/gromacs/top/dgsolv.dat
> >>
> >> Entries in dgsolv.dat: 7
> >>
> >> Opening library file
> >> /homea/scocchi/GROMACS/share/gromacs/top/electroneg.dat
> >>
> >> Entries in electroneg.dat: 71
> >>
> >> Opening library file
> >> /homea/scocchi/GROMACS/share/gromacs/top/elements.dat
> >>
> >> Entries in elements.dat: 218
> >>
> >> Looking whether force field files exist
> >>
> >> Opening library file
> >> /homea/scocchi/GROMACS/share/gromacs/top/ffoplsaa.rtp
> >>
> >> Opening library file
> >> /homea/scocchi/GROMACS/share/gromacs/top/ffoplsaa.n2t
> >>
> >> WARNING: all CONECT records are ignored
> >>
> >> Opening library file
> >> /homea/scocchi/GROMACS/share/gromacs/top/ffoplsaa.n2t
> >>
> >> There are 23 name to type translations
> >>
> >> Generating bonds from distances...
> >>
> >> atom 0
> >>
> >>
> >>
> >> ... and at this point it gets stuck.
> >>
> >>
> >>
> >> Does anyone have a clue about what I am doing wrong? Could it be that
> >> this happens because I am using the most recent version of Gromacs? If
> >> so, what should I modify?
> >>
> >>
> >>
> >> Thank you!
> >>
> >>
> >>
> >> Giulio
> >
> >
> >
> > --
> > Vitaly V. Chaban, Ph.D. (ABD)
> > School of Chemistry
> > V.N. Karazin Kharkiv National University
> > Svoboda sq.,4, Kharkiv 61077, Ukraine
> > email: cha...@univer.kharkov.ua,vvcha...@gmail.com
> > skype: vvchaban, cell.: +38-097-8259698
> > http://www-rmn.univer.kharkov.ua/chaban.html
> > ===
> > !!! Looking for a postdoctoral position !!!
> > ===
> >
>
>
>
> --
> Vitaly V. Chaban, Ph.D. (ABD)
> School of Chemistry
> V.N. Karazin Kharkiv National University
> Svoboda sq.,4, Kharkiv 61077, Ukraine
> email: cha...@univer.kharkov.ua,vvcha...@gmail.com
> skype: vvchaban, cell.: +38-097-8259698
> http://www-rmn.univer.kharkov.ua/chaban.html
> ===
> !!! Looking for a postdoctoral position !!!
> ===
> 

Re: [gmx-users] Re: Groups based on distance criteria

[Vasilii Artyukhov]

2009/7/20 Vitaly V. Chaban 

> Hi Matteus,
>
> Yeah, dynamic groups would be a powerfull tool. But such mechanism is still
> under development if I am not out-of-time.
>
> The possible way to proceed with such kind of research (as Berk advised me
> here long ago) is to sort the trajectory (trjorder) based on the distance
> criteria. Then you can make an index file with N first numbers (which are
> close to the protein) and use g_energy with this group and protein group. It
> seems for your task this way is a perfect solution.
>

Or better yet, use mdrun -rerun on your reordered trajectory and _then_ use
g_energy? This way you would be free of any problems with molecules going in
and out of your solvation shell, if I am getting things right.
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[gmx-users] x2top and OPLS-AA vs. fudged 1-4 interactions

[Vasilii Artyukhov]

Dear colleagues,

I'm looking for clarifications on what exactly I need to do in order to get
a correct scaling of 1-4 interactions for OPLS-AA in a topology made by
x2top. Specifically, will the command

x2top -f in.gro -o out.top

result in a topology that, when fed into grompp, will give a .tpr that is
correct in this respect? Or should I use the same command with the -nopairs
option and let grompp generate the pairs basing on the [ defaults ] section
of ffoplsaa.itp? Or did I miss the correct way to use x2top altogether
(nexcl=4? something with dihedrals? etc.)?

I'm trying to check if OPLS parameters are suitable for the description of a
somewhat unusual system, and so far, the geometry of the system seems to get
distorted by some intramolecular nonbonded interactions; I'd like to know
whether that's because of unsuitable FF parameters, a bad topology, or both
:)

The version of GROMACS is presently 3.3.3, but I'm actually going to use
4.x. for this once I know how to use x2top properly.

Thanks in advance,
Vasilii
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Re: [gmx-users] Is Gromacs CUDA compatible

[Vasilii Artyukhov]

Hi,

Just came across this page:
https://simtk.org/project/xml/downloads.xml?group_id=161#package_id600 - you
might want to check it out :)

2009/2/5 Jagdish S. Varma 

>  Hello,
>
> Can anybody help me. I need to check if Gromacs is CUDA compatible. If not,
> is there any other middle-ware that will make it capable of GPU computing.
> Is CUDA compatibility in the pipeline for Gromacs. Any info would be greatly
> appreciable as I could not find any info on the web.
>
>
>
> *   **[image: image001]*
>
> *Thanks & Regards,
> Jagdish S Varma | Managing Director *
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Re: [gmx-users] Software for ESP fitting

[Vasilii Artyukhov]

2008/9/8 David van der Spoel <[EMAIL PROTECTED]>

> Vasilii Artyukhov wrote:
>
>> Hi gmx-users,
>>
>> Sorry for a not-strictly-GROMACS-related question, but could someone
>> suggest a program I could use to fit atomic charges to quantum chemistry
>> results?
>>
>>  antechamber.


Thanks for a quick response, but does it accept anything except Gaussian
output files as input for RESP? I wonder if I could use cube files for the
procedure...


 Thanks in advance,
>> Vasilii
>>
>>
>> 
>>
>> ___
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>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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[gmx-users] Software for ESP fitting

[Vasilii Artyukhov]

Hi gmx-users,

Sorry for a not-strictly-GROMACS-related question, but could someone suggest
a program I could use to fit atomic charges to quantum chemistry results?

Thanks in advance,
Vasilii
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[gmx-users] Velocity ACF not decaying to zero

[Vasilii Artyukhov]

Dear all,

I'm trying to compare the diffusion constants resulting from g_msd -mol and
g_velacc -mol -nonormalize. The agreement for pure water (512 molecules, 300
K) seems fine (g_analyze output of g_velacc falls into the +- interval of
g_msd), but for a more complex system (4000 waters + 80 small solutes, 290
K), the resulting velocity ACF decays to a nonzero value. This might result
from COM motion, but I think I'm removing it:

; mode for center of mass motion removal
comm-mode= Linear
; number of steps for center of mass motion removal
nstcomm  = 1

Any hints on what this might mean?

Best regards,
Vasilii
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Re: [gmx-users] Re: g_rdf: normalization issues?

[Vasilii Artyukhov]

Thanks!

Ok, so just to be clear, should I expect my RDF to go to 1 or 1-1/N at a
sufficiently large range?

2008/5/8 Berk Hess <[EMAIL PROTECTED]>:

> Hi,
>
> The integrated rdf's never go to 1, since your box has corners which fall
> out of a sphere.
> The normalization should be ok.
> Some time ago the normalization was slightly different, g_rdf normalized
> with the number
> of atoms - 1, if both groups were identical. I removed this in, I think,
> 3.3.2.
>
> Berk.
>
>
>
> --
> Date: Thu, 8 May 2008 15:18:47 +0400
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: g_rdf: normalization issues?
>
>
> Sorry, not Rmax (the box size) but Rmax-Rmin (box size minus size of the
> molecule); still, the integrated RDF values seem to deviate from what
> ithey're supposed to be...
>
> 2008/5/8 Vasilii Artyukhov <[EMAIL PROTECTED]>:
>
> Hi,
>
> I'm using g_rdf 3.3.3 to analyze the distribution of solvent molecules in
> water. What puzzles me is that sometimes in, e.g., two sequential runs, I
> get two RDF's with one of them having *uniformly* larger values than the
> other. Given the fact that the RDF should in principle be normalized, this
> seems very strange. In fact, the intergrated values of RDFs that I get seem
> smaller than 1*Rmax. How is this possible? Is this due to some finite box
> size effect or something else that I'm unaware of?
>
> Best regards, Vasilii
>
>
>
> --
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[gmx-users] Re: g_rdf: normalization issues?

[Vasilii Artyukhov]

Sorry, not Rmax (the box size) but Rmax-Rmin (box size minus size of the
molecule); still, the integrated RDF values seem to deviate from what
ithey're supposed to be...

2008/5/8 Vasilii Artyukhov <[EMAIL PROTECTED]>:

> Hi,
>
> I'm using g_rdf 3.3.3 to analyze the distribution of solvent molecules in
> water. What puzzles me is that sometimes in, e.g., two sequential runs, I
> get two RDF's with one of them having *uniformly* larger values than the
> other. Given the fact that the RDF should in principle be normalized, this
> seems very strange. In fact, the intergrated values of RDFs that I get seem
> smaller than 1*Rmax. How is this possible? Is this due to some finite box
> size effect or something else that I'm unaware of?
>
> Best regards, Vasilii
>
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[gmx-users] g_rdf: normalization issues?

[Vasilii Artyukhov]

Hi,

I'm using g_rdf 3.3.3 to analyze the distribution of solvent molecules in
water. What puzzles me is that sometimes in, e.g., two sequential runs, I
get two RDF's with one of them having *uniformly* larger values than the
other. Given the fact that the RDF should in principle be normalized, this
seems very strange. In fact, the intergrated values of RDFs that I get seem
smaller than 1*Rmax. How is this possible? Is this due to some finite box
size effect or something else that I'm unaware of?

Best regards, Vasilii
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Re: [gmx-users] force field parameters for hydronium

[Vasilii Artyukhov]

Yes, that's exactly the article I had in mind!

There are also people studying stuff like dissociative hydration of, e.g.,
silica, they have some water models that can dissociate when needed, as
well...

http://pubs.acs.org/cgi-bin/abstract.cgi/nalefd/2003/3/i10/abs/nl034480e.html
http://www.rsc.org/Publishing/Journals/DT/article.asp?doi=b516258k

2008/4/28 David van der Spoel <[EMAIL PROTECTED]>:

> Vasilii Artyukhov wrote:
>
> >
> > 2008/4/28 Mark Abraham <[EMAIL PROTECTED]  > [EMAIL PROTECTED]>>:
> >
> >
> > Trying to model hydronium is a pretty flawed thing to do, since the
> >hydrogens in real water are labile - so the molecule you'd label as
> >"hydronium" moves much faster than any atoms do.
> >
> > I actually seem to remember reading something about some dissociative
> > water models that could exchange protons between molecules, so that one
> > could really have something like a pH in the simulation... doesn't really
> > account for the quantum stuff like tunneling, though :)
> >
>
>
> @Article{ Mahadevan2007a,
>  author =   "T. S. Mahadevan and S. H. Garofalini",
>  title ="Dissociative Water Potential for Molecular Dynamics
>  Simulations",
>  journal =  "J. Phys. Chem. B",
>  year = 2007,
>  url =
>
> "http://pubs.acs.org/cgi-bin/abstract.cgi/jpcbfk/asap/abs/jp072530o.html";,
>  doi =  "10.1021/jp072530o",
>  abstract = "A new interatomic potential for dissociative water
>  was developed for use in molecular dynamics
>  simulations. The simulations use a multibody
>  potential, with both pair and three-body terms, and
>  the Wolf summation method for the long-range Coulomb
>  interactions. A major feature in the potential is
>  the change in the short-range O-H repulsive
>  interaction as a function of temperature and/or
>  pressure in order to reproduce the
>  density-temperature curve between 273 K and 373 at 1
>  atm, as well as high-pressure data at various
>  temperatures. Using only the change in this one
>  parameter, the simulations also reproduce
>  room-temperature properties of water, such as the
>  structure, cohesive energy, diffusion constant, and
>  vibrational spectrum, as well as the liquid-vapor
>  coexistence curve. Although the water molecules
>  could dissociate, no dissociation is observed at
>  room temperature. However, behavior of the hydronium
>  ion was studied by introduction of an extra H+ into
>  a cluster of water molecules. Both Eigen and Zundel
>  configurations, as well as more complex
>  configurations, are observed in the migration of the
>  hydronium."
> }
>
>
> >
> > 
> >
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
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>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> [EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
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Re: [gmx-users] force field parameters for hydronium

[Vasilii Artyukhov]

2008/4/28 Mark Abraham <[EMAIL PROTECTED]>:

>  Trying to model hydronium is a pretty flawed thing to do, since the
> hydrogens in real water are labile - so the molecule you'd label as
> "hydronium" moves much faster than any atoms do.


I actually seem to remember reading something about some dissociative water
models that could exchange protons between molecules, so that one could
really have something like a pH in the simulation... doesn't really account
for the quantum stuff like tunneling, though :)
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Re: [gmx-users] Need help with installation on Itanium2

[Vasilii Artyukhov]

Yep, my mistake, I built the serial version using gcc previously, so the
problem really _is_ in Intel's compiler. I've finally figured out how to
make mpicc use gcc instead of Intel, so now I have a working MPI version of
GROMACS.

Thank you again,
Vasilii

2008/4/28 Mark Abraham <[EMAIL PROTECTED]>:

>
> I get the same issue with GROMACS 3.3.2 and 3.3.3 on my Itanium2 system
> using Intel 10.1 icc, and I also get them even without --enable-mpi, e.g.
>
> ../configure --program-suffix=_3.3.3_single --with-fft=fftw2
> --with-external-blas --with-external-lapack
> LIBS="-L/opt/fftw-2.1.5/intel-9.1/lib -lscs"
>
> then make gives
>
> /bin/sh ../../../../libtool   --mode=compile icc -DHAVE_CONFIG_H -I.
> -I../../../../src
> -I../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single
> -I../../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 -w
> -funroll-all-loops -MT nb_kernel010_ia64_single.lo -MD -MP -MF
> .deps/nb_kernel010_ia64_single.Tpo -c -o nb_kernel010_ia64_single.lo
> ../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single/nb_kernel010_ia64_single.S
>  icc -DHAVE_CONFIG_H -I. -I../../../../src
> -I../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single
> -I../../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 -w
> -funroll-all-loops -MT nb_kernel010_ia64_single.lo -MD -MP -MF
> .deps/nb_kernel010_ia64_single.Tpo -c
> ../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_single/nb_kernel010_ia64_single.S
> -o nb_kernel010_ia64_single.o
> /tmp/iccEJOKXd.s(1) : error A2040: Unexpected token: Unary Diez Operator
> at: Start
> ...etc
>
> Running the above icc by hand with -O0 also fails in the same way.
>
>
> Mark
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Re: [gmx-users] Need help with installation on Itanium2

[Vasilii Artyukhov]

Thanks for quick reply,

2008/4/28 Mark Abraham <[EMAIL PROTECTED]>:

> Vasilii Artyukhov wrote:
>
> > Dear everyone,
> >
> > I'm trying to install GROMACS on an Itanium2 cluster using MPI icc. At a
> > certain point, the compilation crashes with
> >
>
> What hardware, compilers, GROMACS version and configure command line were
> you using?


GROMACS 3.3.3, Itanium2, Intel cc version 9.0, MPICH-GM comm lib. As for
configure, nothing interesting, just --disable-nice --enable-mpi CC=icc &
the libs; the serial version (same without --enable-mpi) installs
successfully, so I kind of hope it's only a problem of assembly loops &
Intel's cc.


>
>
> Mark
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[gmx-users] Need help with installation on Itanium2

[Vasilii Artyukhov]

Dear everyone,

I'm trying to install GROMACS on an Itanium2 cluster using MPI icc. At a
certain point, the compilation crashes with

*/bin/sh ../../../../libtool   --mode=compile mpicc -DHAVE_CONFIG_H -I.
-I../../../../src -I/usr/X11R6/include  -I../../../../include
-DGMXLIBDIR=\"/nethome/dvasya/6k//share/top\" -I/nethome/dvasya/6k/include
-O3 -w -MT nb_kernel010_ia64_single.lo -MD -MP -MF
.deps/nb_kernel010_ia64_single.Tpo -c -o nb_kernel010_ia64_single.lo
nb_kernel010_ia64_single.S
 mpicc -DHAVE_CONFIG_H -I. -I../../../../src -I/usr/X11R6/include
-I../../../../include -DGMXLIBDIR=\"/nethome/dvasya/6k//share/top\"
-I/nethome/dvasya/6k/include -O3 -w -MT nb_kernel010_ia64_single.lo -MD -MP
-MF .deps/nb_kernel010_ia64_single.Tpo -c nb_kernel010_ia64_single.S -o
nb_kernel010_ia64_single.o
/tmp/dvasya/iccy1E6hds(1) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/dvasya/iccy1E6hds(2) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/dvasya/iccy1E6hds(3) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/dvasya/iccy1E6hds(4) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/dvasya/iccy1E6hds(5) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/dvasya/iccy1E6hds(6) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/dvasya/iccy1E6hds(7) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/dvasya/iccy1E6hds(8) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/dvasya/iccy1E6hds(10) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/dvasya/iccy1E6hds(15) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/dvasya/iccy1E6hds(193) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/dvasya/iccy1E6hds(195) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/dvasya/iccy1E6hds(269) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/dvasya/iccy1E6hds(423) : error A2040: Unexpected token: Unary Diez
Operator at: Start
/tmp/dvasya/iccy1E6hds(506) : error A2040: Unexpected token: Unary Diez
Operator at: Start
nb_kernel010_ia64_single.o - 15 error(s), 0 warning(s)
make: *** [nb_kernel010_ia64_single.lo] Error 1

*which is something that has actually appeared a couple times on the list
(for instance,
http://www.gromacs.org/pipermail/gmx-users/2007-October/030212.html).
However, the solution to the problem seems to either never have been posted,
or to be far beyond my comprehension. Is there some cure for this?

Best regards,
Vasilii
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Re: [gmx-users] Lipid forcefield to use with TIP5P/OPLSaa

[Vasilii Artyukhov]

Thanks Chris and Mark!

2008/4/21 Chris Neale <[EMAIL PROTECTED]>:

> I use tip4p/opls/berger combination and it works well for me. I have never
> used tip5p. I suggest that you build your membrane and run one control
> simulation (sounds like you would lean toward using spc for this) and then
> one simulation with tip5p. Check order parameters and
> area per lipid while using anisotropic pressure coupling.
>

Surely I'll try to see for myself how bad different water models perform :)
Still, I was hoping that I could get some info beforehand (like if someone
told me that TIP5P absolutely screws up the results for Berger; such kind of
advice can really save one time).

Also, are you sure that you want to use tip5p?
>
> Chris.


I'm afraid I have to use TIP5P; I _am_ looking at temperature dependent
information, and also, I need a good description of hydration of  small
molecules I mentioned. These and other considerations make more or less
every other water model I know of (including TIPxP-Ew) at least twice less
attractive than TIP5P. So if TIP5P doesn't screw up the description of the
membrane as much as any other model would the water part, I think it will
do.

2008/4/22 Marc F. Lensink <[EMAIL PROTECTED]>:

>
> i'm very happily using berger/oplsaa/tip4p.  mind that this means ua
> lipid tails and the rest aa, so unless you have a distinct lipid
> phase, it's probably not what you want.  personally i'm not (yet)
> convinced it's a better combination than berger/gromos/spc, though.
>
> cheers,
> marc
>

I'm sorry, I didn't quite understand the argument about 'having a distinct
phase'. Could you please elaborate?

So, this leaves us with two votes for Berger/TIP4P and nothing at all about
CHARMM27. But it would be really nice to hear from someone who'd been using
the latter FF. (I realize that it might be smarter to ask such questions on
the CHARMM forum, but on the other hand, I'm still willing to do this in
GROMACS...)

Thanks again,
Vasilii
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[gmx-users] Lipid forcefield to use with TIP5P/OPLSaa

[Vasilii Artyukhov]

Dear GROMACS users,

particularly, those experienced with membrane simulations,

I want to simulate lipid bilayers (e.g., DPPC) in the presence of certain
small solutes, much like what was done in A.K. Sum & J.J. de Pablo, Biophys.
J. 85, 3636 (2003) with DMSO. I'd like to use the TIP5P and OPLS all-atom
parameters for water and other stuff, but there's still the question of what
parameters to use for lipids. I'm aware that I'm supposed to do my own
research on this matter, but it'd still be very nice to have some advice on
the choice of parameters from someone with more experience in these things.

>From what I've managed to figure out of Erik Lindahl's tutorial on the
website, I'm basically encouraged to use either Berger parameters, or the
CHARMM27 forcefield (btw, the ffcharm files aren't present on the new
website, had to search the mailing list for a link to the old version) -
unless I know very well what I'm doing, which I obviously don't presently :)
Berger seems to be commonly used in combination with OPLS; however, I get
the impression that it's supposed to work best with SPC, which doesn't suit
my needs really well. As for CHARMM, I'm not really sure if it's supposed to
mix well with OPLS for solutes, and it also seems to be parametrized for use
with TIP3P, not 5P.

So, if anyone could comment on the above questions or point out some of my
misconceptions, this would be greatly appreciated! :)

Thanks,
Vasilii
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Re: [gmx-users] water can't freeze

[Vasilii Artyukhov]

Dear Xiupeng,

What you're seeing is the difference between freezing water and overcooling it.
If you want your water to crystallize, you'll actually have to make it -
e.g., by putting it in contact with ice. Normally, pure water doesn't freeze
on its own, you can easily verify this experimentally at home :)

Best regards,
Vasilii

2008/4/19, Wei, Xiupeng <[EMAIL PROTECTED]>:
>
> Hi gmx users,
>  I'm a new Gromacs user. Till now, I can get pretty good
> simulation of ice melting to water, but why can't I simulate water freezing
> to ice?
>  The .top and .gro files used for water freezing simulation are
> generated by ice melting to 310K. I changed the temperature in .mdp file to
> 230K, but after mdrun, the water was still water, it can't freeze?
>  How can I get water freezing to ice?
> I paste mdp for your reference.
> Thanks.
>
> best,
> xiupeng
>
>
> title= icing at 230 K with cuffoff
> cpp  = /lib/cpp
> integrator   = md
> ;Time step
> dt   = 0.002
> nsteps   = 10
> ;Output control
> nstxout  = 10
> nstvout  = 10
> nstlog   = 100
> nstenergy= 100
> nstxtcout= 100
> ;Neigbour searching
> nstlist  = 10
> ns_type  = grid
> rlist= 0.8
> ;Non bonded interaction
> coulombtype  = pme
> optimize_fft = yes
> fourierspacing   = 0.2
> pme-order= 6
> ewald-rtol   = 1e-05
> rcoulomb = 0.8
> vdw-type = Cut-off
> rvdw = 0.8
> DispCorr = EnerPres
> ;Temperature coupling
> tcoupl   = berendsen
> tc-grps  = System
> tau_t= 0.1
> ref_t= 230
> ;Pressure coupling
> pcoupl   = berendsen
> pcoupltype   = isotropic
> tau_p= 1.0
> compressibility  = 5e-5
> ref_p= 1.0
>
> gen_temp = 230.0
> constraints  = all-bonds
> ; generate velocities
> gen_vel  = yes
> gen_seed = 173529
>
>
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Re: [gmx-users] CPMD and gmx

[Vasilii Artyukhov]

Dear Andrey,

The maximum time step depends on whether you're doing Born-Oppenheimer or
Car-Parrinello MD. In the case of usual BO MD, you normally want a time step
of 0.5-1.0 fs, possibly 2 fs, if you use rigid molecules. In the CP case,
you have to use a much smaller time step to make sure that the electronic
degrees of freedom remain decoupled from the atomic motion (the whole idea
of CP approach is to do more time steps, but with only a single iteration
for the electronic structure at each step instead of a full SCF
minimization). You can find some introductory reading on this, e.g., at the
Dominik Marx group website:
http://www.theochem.ruhr-uni-bochum.de/home.en.html

2008/4/7, Andrey V Golovin <[EMAIL PROTECTED]>:
>
> Dear all,
> We successfully passed all test with CPMD-gmx and now the time to do
> md production runs, In examples from interface home page timestep is
> 1fs but in CPMD papers time step is much less,  about 0.12 fs. Could
> you please advise some papers to read? I found only one paper
> referencing to CPMD-gmx interface publication. Is any common settings
> for metal cations?
> The best that I found is links from
> http://www.cpmd.org/cpmd_publications.html.
> Thanks for any comment.
> --
> Best regards, Andrey
>
> 
> Andrey V. Golovin
> Ph.D, Assistant professor tel: +7 (495) 939-5305
> Bioengineering and
> Bioinformatics Department
> Moscow State University fax: +7 (495) 939-3181
> 119992 Moscow E-mail: [EMAIL PROTECTED]
> Russia web: http://rnp-group.genebee.msu.su
>
> 
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Re: [gmx-users] POL3 polarizable water model

[Vasilii Artyukhov]

I believe the manual says that only the shell-on-a-spring model is supported
by GROMACS for polarization. As far as I can recall, the POL3 model uses
atomic multipoles, so tough luck for you...

2008/3/25, Bo Zhou <[EMAIL PROTECTED]>:
>
> Dear Gromacs users,
>
> I wonder whether or not the POL3 polarizable water model (Caldwell JW,
> Kollman PA (1995) J Phys Chem 99: 6208-6219.) can be incorporated in gmx
> with amber03 force field. Thanks in advance.
>
> Best regards
>
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Re: [gmx-users] g_rdf -[no]com

[Vasilii Artyukhov]

Ok, thanks!

2008/1/11, Berk Hess <[EMAIL PROTECTED]>:
>
>
>
>
> 
> > Date: Fri, 11 Jan 2008 15:58:23 +0100
> > From: [EMAIL PROTECTED]
> > To: gmx-users@gromacs.org
> > Subject: Re: [gmx-users] g_rdf -[no]com
> >
> > Oh yes, the -rdf option! And the run input file! That makes me feel
> kinda stupid... Thank you very much & sorry for the dumb questions.
> >
> > But still, having read the help again, I don't quite get the logic
> behind g_rdf -com -rdf atom -n -s giving me an all-zero output for the RDF
> between the COM of the molecule and water oxygen (which is I suppose what I
> request it to produce). However, using -rdf mol_com seems to work fine.
>
> The output should be the same, but there is a bug in g_rdf -com.
> I have fixed it for the next release.
>
> Berk.
>
> _
> Express yourself instantly with MSN Messenger! Download today it's FREE!
>
> http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___
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Re: [gmx-users] g_rdf -[no]com

[Vasilii Artyukhov]

Oh yes, the -rdf option! And the run input file! That makes me feel kinda
stupid... Thank you very much & sorry for the dumb questions.

But still, having read the help again, I don't quite get the logic behind
g_rdf -com -rdf atom -n -s giving me an all-zero output for the RDF between
the COM of the molecule and water oxygen (which is I suppose what I request
it to produce). However, using -rdf mol_com seems to work fine.

2008/1/11, David van der Spoel <[EMAIL PROTECTED]>:
>
> Vasilii Artyukhov wrote:
> > Hi everybody,
> >
> > I'm dealing with aqueous solutions of some small molecules. Just to
> clarify:
> >
> > 1) When I type g_rdf, is the -com option on by default? g_rdf -h makes
> > me suspect it is...
> read again.
>
> > 2) When I type g_rdf -nocom, what point of the molecule does the
> > resulting RDF correspond to?
> it works between atoms unless you use one of the other options.
>
> > 3) g_rdf -h says that the -com option makes it calculate the RDF w.r.t.
> > the COM of the 1st molecule. What about the other one, how is it
> treated?
> >
> have you tried it out at all?
>
> From g_rdf -h:
> The option -rdf sets the type of rdf to be computed. Default is for
> atoms or particles, but one can also select center of mass or geometry
> of molecules or residues. In all cases only the atoms in the index
> groups are taken into account. For molecules and/or the center of mass
> option a run input file is required. Other weighting than COM or COG can
> currently only be achieved by providing a run input file with different
> masses. Option -com also works in conjunction with -rdf.
>
> > Thanks in advance,
> > Vasilii
> >
> >
> > 
> >
> > ___
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>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> [EMAIL PROTECTED][EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] g_rdf -[no]com

[Vasilii Artyukhov]

Hi everybody,

I'm dealing with aqueous solutions of some small molecules. Just to clarify:

1) When I type g_rdf, is the -com option on by default? g_rdf -h makes me
suspect it is...
2) When I type g_rdf -nocom, what point of the molecule does the resulting
RDF correspond to?
3) g_rdf -h says that the -com option makes it calculate the RDF w.r.t. the
COM of the 1st molecule. What about the other one, how is it treated?

Thanks in advance,
Vasilii
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Re: [gmx-users] Gromacs-MPI cygwin

[Vasilii Artyukhov]

Just a thought... Maybe you should instead try WMPI (or whatever the thing
is called, you know, MPI for Windows...) and some of the Windows ports of
GROMACS that you can find in the user contributions area of the website.
That's supposing you really _need_ to use MPI, of course :)

In my case, though, the problem was solved by installing Linux.

2007/12/22, [EMAIL PROTECTED] <[EMAIL PROTECTED]>:
>
> Hi,
> I would like to compile gromacs using cygwin and mpi on a machine
> running win2003 server, with two quad-core processor.
> Does anybody experince in this type of situation. I have some problem
> compiling mpi, becouse I'm able to run the configure script with
> "without-romio" option, but the process make fails.
> Thanks a lot
>
> Jacopo
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[gmx-users] GROMACS and GPU (and PS3)

[Vasilii Artyukhov]

Hi everybody,

I wonder if GROMACS will eventually support running on the graphics cards,
especially since there have been several announcements of extremely powerful
cards like AMD's FireStream recently. I know that the question has
repeatedly been asked some time ago, but hey, the Stanford guys from [EMAIL 
PROTECTED] did
manage to adapt GROMACS for GPUs, and they don't seem to regret it :)

I'd also like to know if anyone has actually tried running GROMACS on
PlayStation 3, seems like this Cell CPU could perform really well for
moderately sized systems (so that you don't run into the 512 MB memory
limitation)...


Best regards,
Vasilii
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Re: [gmx-users] fullerene topology

[Vasilii Artyukhov]

2007/12/5, Adam Fraser <[EMAIL PROTECTED]>:
>
>
> I just need accurate partial charges to build the topology file with.


Well, if you really meant what your message said, the answer should be
exactly 0.0 a.u. on every atom.
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Re: [gmx-users] GROMACS in parallel on a multicore PC?

[Vasilii Artyukhov]

Thanks for the quick response :)
2007/11/21, Carsten Kutzner <[EMAIL PROTECTED] >:
>
> Hi Vasilii,
>
>
> > - Does GROMACS support multithreaded execution & how efficient is it?
> As far as I know this is planned, but not supported yet.

Ok, but what about the underlying math libs? Would using threaded libs boost
performance to any noticeable extent?
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[gmx-users] GROMACS in parallel on a multicore PC?

[Vasilii Artyukhov]

Hi everybody,

Sorry for a somewhat technical question, but I'd like to know which is the
best way to run GROMACS on a SMP machine (in particular, a multicore PC).
The (known) points of interest are:

- Does GROMACS support multithreaded execution & how efficient is it?

- Should I rather use some kind of MPI & which (LAM/Open/MPICH) is better &
why?

Surely, there's always the option to run two serial jobs instead with a
greater efficiency, but having some means to boost the single job
performance by something like 1.9x would be very useful...

Thanks in advance,

Vasilii
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Re: [gmx-users] queue up simulations

[Vasilii Artyukhov]

Hi,

I think what you're looking for is called a shell script :)

26 Oct 2007 06:01:31 -, sarbani chattopadhyay <
[EMAIL PROTECTED]>:
>
>   hi,
>
> I want to know is there any way to 'queue up mdrun jobs' so that once
> one job is
> finished, the next starts automaticaly?
>
> Thanks in advance.
>
> Sarbani
>
>
> [image: 
> Naukri]  PROTECTED]/1503566_1496716/1502982/1?PARTNER=3&OAS_QUERY=null+target=new+>
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Re: [gmx-users] Rerefence on Berendsen vs. Nose-Hoover

[Vasilii Artyukhov]

There's a reference in the manual, where the T-coupling schemes are first
introduced.

2007/10/15, Jochen Hub <[EMAIL PROTECTED]>:
>
> Hi,
>
> I think there is a paper around which says that for parcticle purposes
> it hardly matters whether one uses Berendsen or Nose-Hoover T-coupling.
> Does anyone remember the reference?
>
> Thanks in advance,
> Jochen
>
> --
> 
> Jochen Hub
> Max Planck Institute for Biophysical Chemistry
> Computational biomolecular dynamics group
> Am Fassberg 11
> D-37077 Goettingen, Germany
> Email: jhub[at]gwdg.de
> 
>
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Re: [gmx-users] Help for simulating the metalcluster

[Vasilii Artyukhov]

Sorry for advertising a competitor code on the list :) but you might want to
check out the DL_POLY package, as well...

2007/10/1, Utpal Sarkar <[EMAIL PROTECTED]>:
>
> Dear Gromacs Users,
>I want to use GROMACS code to simulate the metal cluster
> (say Iron or Na) on
> substrate (say silicon). I want to optimize the structures actually. (I
> have optimized some metal cluster.
> using gaussian software so I know the geometry of the cluster, I mean the
> XYZ coordinate of the atoms).
> But I want to optimized it using GROMACS. So is it possible using GROMCS?
> If yes, then HOW?
>
> I also want to know is there any option in the code where I can implement
> my own potential energy
> function (or force field)? (I have seen Chapter 6, Item 6.6.2, but I could
> not able to understand whether
> is it sufficient to implement Second Moment Approximation [SMA] type
> potential here?).
> So is it possible to use implemet SMA type potential for metals in
> GROMACS?
>
> I will be highly obliged if you can give me some advise regarding this.
>
> Thanking you in advance
> With best regards
> Utpal Sarkar
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Re: [gmx-users] Troubles with genbox and random insertion

[Vasilii Artyukhov]

That's the whole idea, you _have_ to change the seed value, since it's used
by the program to generate a sequence of pseudorandom numbers...

2007/9/18, Shay Amram <[EMAIL PROTECTED]>:
>
> Greetings Ran,
>
> I tried to add the –seed flag as you said, at the end of each genbox (with
> different various numbers), and it doesn't help.
>
> (ran the following command:)
>
> *genbox -cp cent_tim.gro -ci plm.gro -nmol 4 -o 1PLM_tim.gro –seed 4*
>
>
>
> Each time I change the number after "-seed" I get a different GRO file,
>
> But no matter how many time I run genbox with the same number after
> "-seed" I always get the same GRO file in the end.
>
>
>
> Is it possible that there's something wrong in the system settings?
> Something that has to do with the way genbox chooses random numbers?
>
>
>
> Thanks,
>
> -Shay
>
>
>
>
> --
>
> *From:* [EMAIL PROTECTED] [mailto:
> [EMAIL PROTECTED] *On Behalf Of *Ran Friedman
> *Sent:* Tuesday, September 18, 2007 14:40
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] Troubles with genbox and random insertion
>
>
>
> Dear Shay,
>
> Use the -seed flag
>
> Ran.
>
> Shay Amram wrote:
>
> Dear Gromacs users
>
>
>
> I'm having a bit of a trouble with genbox: I want to insert 4 PLM
> (palmitate) molecules at random positions in my simulation.
>
> So I tried running:
>
> *genbox -cp cent_tim.gro -ci plm.gro -nmol 4 -o 4PLM_tim.gro -seed 100*
>
> *pdb2gmx -f 4PLM_tim.gro -o 4PLM_tim.gro -p –ter*
>
> * *
>
> I got a GRO file and indeed there were 4 PLM molecules.
>
> *When I ran the same script again, I got the exact same GRO file.*Meaning, 
> the positioning of the PLM molecules wasn't truly random.
>
>
>
> After reading the Description on
>
> http://www.gromacs.org/documentation/reference/online/genbox.html
>
> I saw that the –ci flag supposedly works only if I insert one molecule.
>
>
>
> So I tried a different approach – to add a single PLM four times like so:
>
> *# Palmitate No.1*
>
> *genbox -cp cent_tim.gro -ci plm.gro -nmol 4 -o 1PLM_tim.gro*
>
> *pdb2gmx -f 1PLM_tim.gro -o 1PLM_tim.gro -p -ter*
>
> * *
>
> *# Palmitate No.2*
>
> *genbox -cp 1PLM_tim.gro -ci plm.gro -nmol 1 -o 2PLM_tim.gro*
>
> *pdb2gmx -f 2PLM_tim.gro -o 2PLM_tim.gro -p -ter*
>
> * *
>
> *# Palmitate No.3*
>
> *genbox -cp 2PLM_tim.gro -ci plm.gro -nmol 1 -o 3PLM_tim.gro*
>
> *pdb2gmx -f 3PLM_tim.gro -o 3PLM_tim.gro -p -ter*
>
> * *
>
> *# Palmitate No.4*
>
> *genbox -cp 3PLM_tim.gro -ci plm.gro -nmol 1 -o 4PLM_tim.gro*
>
> *pdb2gmx -f 4PLM_tim.gro -o 4PLM_tim.gro -p –ter*
>
> * *
>
> I got a different GRO than the one I got when adding the whole 4 of PLM in
> one line,
>
> but still, If I run the same batch of commands again, I get the same GRO
> file.
>
> If I run the first batch 50 times, each time I'll get the same GRO file as
> before.  Same is true for the second batch. Meaning the positioning is not
> random.
>
>
>
> I tried fiddling with it some more (removing "-seed 100" etc., ) and still
> the result is the same.
>
>
>
> Thank you very much in advance and best regards,
>
> Shay Amram
>
>
>
>
> --
>
> --
>
> Ran Friedman
>
> Postdoctoral Fellow
>
> Computational Structural Biology Group (A. Caflisch)
>
> Department of Biochemistry
>
> University of Zurich
>
> Winterthurerstrasse 190
>
> CH-8057 Zurich, Switzerland
>
> Tel. +41-44-6355593
>
> Email: [EMAIL PROTECTED]
>
> Skype: ran.friedman
>
> --
>
>
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