Re: [gmx-users] trr files transferability

[Mark Abraham]

On 24/02/2011 9:44 AM, Ravi Bhadauria wrote:

Hi all,

I have a simple question about trr files. Are they transferable across 
different version(s), and more importantly, different bit 
architectures (32bit to 64bit and vice versa). Please let me know.


All GROMACS file formats are insensitive to endian-ness or machine word 
size. The .tpr and .cpt file formats are versioned and fully 
backward-compatible. So you can't run a new .tpr on an old mdrun.


Mark
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[gmx-users] trr files transferability

[Ravi Bhadauria]

Hi all,

I have a simple question about trr files. Are they transferable across
different version(s), and more importantly, different bit architectures
(32bit to 64bit and vice versa). Please let me know.

Thanks in advance.

Ravi Bhadauria
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[gmx-users] Re: PMF from pull code, unexpected results

[Michael Brunsteiner]

chris.neale at utoronto.ca wrote:

> Looking at http://www.brunsteiner.net/tbut-pmf.gif you seem to be getting 
>exactly what I would
> expect. The difference is the entropy term. Note that the spherical shell 
>increases volume as r
> increases for pulldim YYY but this effect is absent for pulldim NNY. This is 
>why you can correct
> as per an RDF.

The "entropy term" (Eqn 6.1 in the manual) has already been the source
of some confusion in this list ... 

If you make a "Gedankenexperiment" and consider the PMF between two atoms in 
vacuum 

that interact ONLY through a simple radial, for example a LJ, potential, and 
then calculate the PMF 

using the pull-code ...  if you don't do umbrella sampling + WHAM but instead 
use constraints 

(pull = constraint) you can do the calculation in your head, to find that the 
resulting PMF 

is, of course, nothing else but the original LJ potential. And you will get the 
SAME result
if you do this calculation in one or in three dimensions (pulldim NNY or 
pulldim 
YYY)
so where does the entropy and the correction term in eqn 6 come in here??

In Section 6.1 of the manual it says: "But when calculating a PMF between two 
solutes in a
solvent, for the purpose of simulating without solvent, the entropic 
contribution should be removed."
I find this a bit confusing, first ... "simulating without solvent" ... why 
would that be
my (or anybodies) purpose? and second:

according to eqn 6.1 this "entropic contribution" is: PMF(r) = - (nc-1)kBT 
log(r)

for this to make sense r would have to be dimensionless wouldn't it?
I could divide r by the distance at which i arbitrarily chose my PMF to vanish,
call it r_c, which would have the advantage that then the correction is zero at 
this
distance ... but then this is just wild guess of mine ... anyway, that would 
mean 

that, if I call the PMF coming out of mdrun/g_wham PMF_wham, 
then the "true" PMF is: PMF(z) = PMF_wham (z) + (nc-1)kBT log(z/r_c)
(the plus comes from the double minus, as in: "removing" something thats 
negative)

is that correct? ... and if so, why does it, seemingly, not apply in the above 
Gedankenexperiment?

Yours truly (and maybe some other people) would really appreciate if somebody 
in 
the know
would clarify that!

thanks in advance!

Michael


  
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[gmx-users] widom insertion

[Thomas Koller]

Hello, 

is Widom test particle insertion and with that, the calculation of solubility 
in Gromacs possible?

Regards,
Thomas
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Re: [gmx-users] Interatomic distance matrices

[Tsjerk Wassenaar]

Hi Nathan,

g_rmsdist gives full matrices, and in .xpm format for which you'd need
to do more scripting than for your original problem :)
But you might find genrestr useful. It can generate constraints for
all distances in a selection, which means you get a half matrix with
the distances. They're not going to be formatted as a half matrix
though. Maybe take these 15 minutes to script it...

Cheers,

Tsjerk

On Wed, Feb 23, 2011 at 7:47 PM, J. Nathan Scott
 wrote:
> Dear Gromacs users,
>
> I was wondering, is there any utility in Gromacs for calculating and
> saving a triangular matrix of interatomic distances from a trajectory
> frame? The website mailing list search seems to be down, and Google
> has not been of much help. g_rmsdist looks like it *might* be able to
> do this, but from the documentation I can't tell whether or not there
> is a set of switches that would allow one to turn off the
> averaging/rms calculation features and instead generate a single frame
> static distance matrix.
>
> If Gromacs can't do this, can anyone recommend another program that
> could generate such matrices? This would not be hard to code, but time
> savers are always appreciated. :)
>
> Best Wishes,
> Nathan
>
> --
> J. Nathan Scott, Ph.D.
> Postdoctoral Fellow
> Department of Chemistry and Biochemistry
> Montana State University
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> gmx-users mailing list    gmx-users@gromacs.org
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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[gmx-users] Interatomic distance matrices

[J. Nathan Scott]

Dear Gromacs users,

I was wondering, is there any utility in Gromacs for calculating and
saving a triangular matrix of interatomic distances from a trajectory
frame? The website mailing list search seems to be down, and Google
has not been of much help. g_rmsdist looks like it *might* be able to
do this, but from the documentation I can't tell whether or not there
is a set of switches that would allow one to turn off the
averaging/rms calculation features and instead generate a single frame
static distance matrix.

If Gromacs can't do this, can anyone recommend another program that
could generate such matrices? This would not be hard to code, but time
savers are always appreciated. :)

Best Wishes,
Nathan

--
J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University
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Re: [gmx-users] Website search broken

[Olga Ivchenko]

I also have the same problem with the search.

Olga

2011/2/23 Emine Deniz Tekin 

> Hi Justin,
>
> No matter what I search at gromacs search field, it gives the same error
> message.
> Deniz
>
>
> On Wed, Feb 23, 2011 at 3:58 PM, Justin A. Lemkul  wrote:
>
>>
>> Hi,
>>
>> Is anyone else having problems using the search feature on the Gromacs
>> site?  If I search for "tutorials," I get:
>>
>> Your advanced search query is not formatted properly, and thus was not
>> understood by the search engine. Please consult our documentation on
>> supported search operators.
>> Table './gromacs_wikidb/query_log' is marked as crashed and should be
>> repaired
>> tutorials
>>
>> I know that this search should work, so I figured it was a robust test.
>> Anything else I search for gives me an analogous result.
>>
>> -Justin
>>
>> --
>> 
>>
>> 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
>>
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] Website search broken

[Emine Deniz Tekin]

Hi Justin,

No matter what I search at gromacs search field, it gives the same error
message.
Deniz

On Wed, Feb 23, 2011 at 3:58 PM, Justin A. Lemkul  wrote:

>
> Hi,
>
> Is anyone else having problems using the search feature on the Gromacs
> site?  If I search for "tutorials," I get:
>
> Your advanced search query is not formatted properly, and thus was not
> understood by the search engine. Please consult our documentation on
> supported search operators.
> Table './gromacs_wikidb/query_log' is marked as crashed and should be
> repaired
> tutorials
>
> I know that this search should work, so I figured it was a robust test.
> Anything else I search for gives me an analogous result.
>
> -Justin
>
> --
> 
>
> 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
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] Website search broken

[Justin A. Lemkul]

Hi,

Is anyone else having problems using the search feature on the Gromacs site?  If 
I search for "tutorials," I get:


Your advanced search query is not formatted properly, and thus was not 
understood by the search engine. Please consult our documentation on supported 
search operators.

Table './gromacs_wikidb/query_log' is marked as crashed and should be repaired
tutorials

I know that this search should work, so I figured it was a robust test. 
Anything else I search for gives me an analogous result.


-Justin

--


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] Residue 'DEF' not found in residue topology database

[Justin A. Lemkul]

Emine Deniz Tekin wrote:


Hi gromacs users,


I am using the gromacs 4.5.3 version. I created a lipopetide which 
consist of 12 Carbon atoms (tail) connected to 
Val-Val-Ala-Gly-Glu-Arg-Gly-Asp (residues) using ARGUSLAB and I saved it 
as a pdb file.


Then, when I used the following command in gromacs:

 pdb2gmx   –flipopepArgus.pdb(GROMOS96 45a3 force field&spc type water 
model)

 I got the following error message:

 Fatal error:

Residue 'DEF' not found in residue topology database

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors

 

As far as I could understand, there is no problem with the residues 
 but  there is a problem with the atoms in the tail (12 Carbon atoms, 23 
Hydrogen atoms and an Oxygen atom, actually it is called a lauroic 
acid). These atoms are defined as DEF.  I thought  I should  rename the 
pdb to the expected name given in the .rtp file of  the 45a3 force field 
for my lipopeptide. But I could not find a parameterization for the 
 lauroic acid. In this case, what shoul I do?



At the 
 http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blocks 
page, I found;



*Abbrev.*



*Source*



*2*



*Full Name*



*Formula*



*Specifics*

LAU



fa.itp



O



lauroic acid



C_11 H_23 COOH



-

 


Does using fa.itp file solve my problem? If yes, where can I get this file?




This topology is from the deprecated Gromos87 (hacked) force field called ffgmx. 
 Don't use it.  The reasons are described in the manual.  What's more, you 
can't use a standalone topology if your molecule is covalently linked to a 
peptide.  You can't have bonds between different [moleculetypes] (i.e. between 
topologies) in Gromacs.


The proper procedure is to parameterize the lauroic acid:

http://www.gromacs.org/Documentation/How-tos/Parameterization

or obtain compatible parameters from elsewhere and implement them in your chosen 
force field:


http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

You could use Berger lipid parameters for the lauroic acid moiety, you'll just 
have to add this residue to the force field.  The membrane protein tutorial I 
wrote will walk you through how to modify the force field properly.


http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations

-Justin


I would be so glad if you can help me solve this problem.
Thank you in advance,

Deniz



--


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] Can g_wham support using different temperature for different windows?

[Justin A. Lemkul]

Jianguo Li wrote:

Dear all,
 
Thank you all for your suggestions or comments to my problem. Now I am 
planning to extend my simulations or using REMD in those bad windows to 
get converged PMF.
I have another question: if I extend the umbrellar simulation to 1 
microsecond only in those problematic windows, while running shorter 
simulation (e.g., 100 ns) in those windows far away from the 
membrane. Does g_wham accpet using diffrent simulation time for 
different windows?


Theoretically, but if you are going to discard any of the initial time (that is, 
equilibration in each window) by using the -b option, you'll have to make sure 
that you don't eliminate windows by doing so, i.e. 100 ns in some windows and 1 
us in others, using g_wham -b 20 would completely neglect any windows with 
shorter time and basically make the PMF curve useless.


-Justin


Thank you in again,
 
Cheers,
Jianguo 



*From:* XAvier Periole 
*To:* Discussion list for GROMACS users 
*Sent:* Wednesday, 23 February 2011 20:59:18
*Subject:* Re: [gmx-users] Can g_wham support using different 
temperature for different windows?



On Feb 23, 2011, at 3:21 AM, Jianguo Li wrote:



Thank you  for the the useful information, XAvier.
My peptide is highly positively charged, 18 AA with +12 charges. Other 
of my group members told me their NMR experiment in water indicates 
the peptide conformation is very dynamics. Actually I also did peptide 
refolding using REMD in water, and I found it is flexible and has no 
stable structure in water, except some instantaneously helical 
structures. In addition, my peptide consists of two branches connected 
by unnatural peptide bond, so the backbone is discontinuous, and also 
because of the high charges, I assume the peptide doesn't form helcial 
structure in the negatively charged membrane. Therefore I didn't put 
any constraints in the peptide to keep the secondary structure of the 
peptide. I know there are assumptions in my model, but I have no other 
information to increase the accuracy of the model.  In fact, when I am 
doing REMD folding simulations using Gromos53a6 and CHARMM27 with 
cMap, I got different results. But the common thing is that both 
results seems to indicate the peptide is filexbile in water without 
stable secondary structure. Then I used MARTINI FF with flexible 
structure, just to find some general features.


I will try your suggestion, doing REMD in those bad windows.
 
And the reference you mentioned is very useful, I will take a look at 
them :-)


Another question: Suppose some other tools support using different 
temperatures in different windows, as you mentioned, if 500K is too 
high to have a significant contribution to the probability of 300K,  
can I do a series of simulation in a certain window with different 
temparatures (e.g. 300K, 350K, 400K,450K, 500K). In such cases, in 
each window, I need to do 5 simulations, which will be much cheaper 
than doing REMD in that window. 
It would be computationally cheaper but this is assuming that you'd get 
the info you are looking for within these simulations and again the 
weight of the conformations from 400/450/500 K at 300 K is questionable. 
Note also that the conformations sampled at high temperature with 
position restrains on the lipids to avoid deformation will be difficult 
to interpret! 


Cheers
Jianguo



*From:* XAvier Periole mailto:x.peri...@rug.nl>>
*To:* Discussion list for GROMACS users >

*Sent:* Tuesday, 22 February 2011 21:18:12
*Subject:* Re: [gmx-users] Can g_wham support using different 
temperature for different windows?



A few notes:
- the original method (Kumar-JCC-1992) that inspired wham was actually 
developed to mix different temperature simulations. It is however not 
clear 
for the type of system you are simulating how much a 500K simulation 
would be useful to improve the sampling at 300 K or so. The reason is 
that the enthalpy difference between the two systems is so high that the 
probability that a conformation from a 500K simulation would contribute
to sampling at 300K is really low. It would much more efficient for 
systems 
with implicit solvent for which the energy of the system does not vary so 
much with the temperature. One could look at Chodera-JCTC-2007 
and ref therein for a few examples.

- I would think that a REMD simulation would be more useful. No need to
run 30 replicas to very hight temperature! A bilayer at 500K might get 
funny.


- Martini force field for flexible regions of protein should not be 
trusted ... or
really interpreted with a lot of reserve. The "coil" definition is 
simply something
flexible with absolutely no guaranty that it could be representing 
some thing 
even close to reality, which we have only an approximate idea of what 
it is! 

- A peptide in a bilayer has a

Re: [gmx-users] Can g_wham support using different temperature for different windows?

[Jianguo Li]

Dear all,

Thank you all for your suggestions or comments to my problem. Now I am planning 
to extend my simulations or using REMD in those bad windows to get converged 
PMF. 

I have another question: if I extend the umbrellar simulation to 1 microsecond 
only in those problematic windows, while running shorter simulation (e.g., 100 
ns) in those windows far away from the membrane. Does g_wham accpet using 
diffrent simulation time for different windows?
Thank you in again,

Cheers,
Jianguo 





From: XAvier Periole 
To: Discussion list for GROMACS users 
Sent: Wednesday, 23 February 2011 20:59:18
Subject: Re: [gmx-users] Can g_wham support using different temperature for 
different windows?



On Feb 23, 2011, at 3:21 AM, Jianguo Li wrote:


>Thank you  for the the useful information, XAvier.
>My peptide is highly positively charged, 18 AA with +12 charges. Other of my 
>group members told me their NMR experiment in water indicates the peptide 
>conformation is very dynamics. Actually I also did peptide refolding using 
>REMD 
>in water, and I found it is flexible and has no stable structure in water, 
>except some instantaneously helical structures. In addition, my peptide 
>consists 
>of two branches connected by unnatural peptide bond, so the backbone is 
>discontinuous, and also because of the high charges, I assume the peptide 
>doesn't form helcial structure in the negatively charged membrane. Therefore I 
>didn't put any constraints in the peptide to keep the secondary structure of 
>the 
>peptide. I know there are assumptions in my model, but I have no other 
>information to increase the accuracy of the model.  In fact, when I am doing 
>REMD folding simulations using Gromos53a6 and CHARMM27 with cMap, I got 
>different results. But the common thing is that both results seems to indicate 
>the peptide is filexbile in water without stable secondary structure. Then I 
>used MARTINI FF with flexible structure, just to find some general features.
>
>I will try your suggestion, doing REMD in those bad windows.
> 
>And the reference you mentioned is very useful, I will take a look at them :-)
>
>Another question: Suppose some other tools support using different 
>temperatures 
>in different windows, as you mentioned, if 500K is too high to have a 
>significant contribution to the probability of 300K,  can I do a series of 
>simulation in a certain window with different temparatures (e.g. 300K, 350K, 
>400K,450K, 500K). In such cases, in each window, I need to do 5 simulations, 
>which will be much cheaper than doing REMD in that window. It would be 
>computationally cheaper but this is assuming that you'd get the info you are 
>looking for within these simulations and again the weight of the conformations 
>from 400/450/500 K at 300 K is questionable. Note also that the conformations 
>sampled at high temperature with position restrains on the lipids to avoid 
>deformation will be difficult to interpret! 

>Cheers
>Jianguo
>
>
>
>
>

From: XAvier Periole 
>To: Discussion list for GROMACS users 
>Sent: Tuesday, 22 February 2011 21:18:12
>Subject: Re: [gmx-users] Can g_wham support using different temperature for 
>different windows?
>
>
>
>
>A few notes:
>- the original method (Kumar-JCC-1992) that inspired wham was actually 
>developed to mix different temperature simulations. It is however not clear 
>for the type of system you are simulating how much a 500K simulation 
>would be useful to improve the sampling at 300 K or so. The reason is 
>that the enthalpy difference between the two systems is so high that the 
>probability that a conformation from a 500K simulation would contribute
>to sampling at 300K is really low. It would much more efficient for systems 
>with implicit solvent for which the energy of the system does not vary so 
>much with the temperature. One could look at Chodera-JCTC-2007 
>and ref therein for a few examples.
>- I would think that a REMD simulation would be more useful. No need to
>run 30 replicas to very hight temperature! A bilayer at 500K might get funny.
>
>
>- Martini force field for flexible regions of protein should not be trusted 
>... 
>or
>really interpreted with a lot of reserve. The "coil" definition is simply 
>something
>flexible with absolutely no guaranty that it could be representing some thing 
>even close to reality, which we have only an approximate idea of what it is! 
>
>
>- A peptide in a bilayer has a very high chance to get into a helical 
>conformation.
>Do you think it is reasonable to keep it "flexible"? 
>
>
>- As noted by Justin and Chris, you definitely have a problem of convergence 
>... 
>I am not sure how many "converged" examples of PMFs of peptide crossing a
>bilayer are out in the literature (Justin?) but from our experience with 
>Martini 
>it does take an awful lot of time to really get convergence. For you system I 
>would expect at least a microsecond for the windows wh

[gmx-users] %exist hydrogen bond

[leila karami]

Dear Justin

very thanks for your time and attention.

I checked my input files again. there was problem in .pdb file.

correction of .pdb file results in output file being as follows (previous
problem was solved):

#Donor   Acceptor   %
Exist.

  0.160
  NGL1 NSOL2225OW 0.400
 ARG58   NH2   SOL3827OW 43.565
 ARG58   NH2   SOL7338OW 1.839
 ARG58   NH1   SOL2225OW 0.080
 ARG58   NH1   SOL2253OW  21.663
 ARG58   NH1   SOL7338OW 0.160
 ARG58NE   SOL3595 OW   1.359
   SOL1043OW  GLY3  O 1.759
   SOL1043OW  GLY4  O 0.400
   SOL1548OW THR47 O61.711
   SOL1548OW ASN51   OD1 16.867
   SOL1548OW ASN51   ND2  0.320
   SOL1805OW GLN23   OE1 11.191
   SOL1805OW LEU26 O0.160
   SOL1805OW SER27 N0.160

best regards

-- 

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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Re: [gmx-users] Can g_wham support using different temperature for different windows?

[Jianguo Li]

Thanks for your comments, Patric.

You are right. The energy barrier is too high for charged groups to translocate 
the hydrophobic region of the membrane. And my peptide contains 12 positively 
charge residues (ARG and LYS), therefore it is unlikely to sample those 
translocation. I am considering to extend my simulations to microsecond level 
or 
longer or use REMD.

Cheers,
Jianguo



From: Patrick Fuchs 
To: Discussion list for GROMACS users 
Sent: Wednesday, 23 February 2011 19:04:05
Subject: Re: [gmx-users] Can g_wham support using different temperature for 
different windows?

Hi,
I think your PMF is asymetric because your peptide is asymetric and you don't 
sample enough. To get a symetric PMF, your peptide would have to sample all the 
possible conformations *and* orientations in each window. Thus it means that 
for 
the windows in the center of the bilayer (where you say it's extended and 
interacts with the two monolayers) it'll have to rotate completely the other 
way 
round. This event will probably be *very* rare because you have to translocate 
positive charges across the membrane which cost ~ 40 to 50 kJ/mol (see the PMF 
of Lys+ and Arg+ in 10.1021/ct700324x).
So as suggested by Chris, Justin and Xavier, you'll have to sample way more 
than 
100 ns per window. I think you should go at least to the microsecond time scale 
(or more?). Or maybe starting from different initial conformations/orientations 
for a given window and then concatenate the different trajectories?
Also consider the remark of Xavier, TM or interfacial peptides are most of the 
time alpha-helical within the membrane. So far in literature, PMFs of a whole 
peptide across a bilayer were done by restraining the peptide in a helical 
conformation (e.g. 10.1016/j.bpj.2010.12.3682). It is anyway a very difficult 
problem (and probably impossible at atomistic resolution) to get a converged 
PMF 
for a whole peptide (e.g. 10.1016/j.bpj.2009.03.059).
Ciao,

Patrick

Le 23/02/2011 05:25, Jianguo Li a écrit :
> Sorry, why do you think the PMF should be asymmetric?
> 
> I pulled my peptide from d=9nm (above the membrane) to d=-3nm (below the
> membrane) and I did windowed umbrella sampling in the range of d=-1.05nm
> to d=9nm. At least the PMF should be symmetric with respect of the
> bilayer center in the range of d=[-1.05nm 1.05nm], something like a
> guassian distribution. But I got asymmetric PMF in this region. I also
> did reverse pulling starting from the peptide below the membrane ending
> with the peptide above the membrane. And the subsequent PMF of reversed
> pulling is also asymmetic.
> 
> I have position restrains of the phosphate beads of the lipids in
> z-direction. So the membrane should be stable in REMD. But as you
> mentioned, if peptide is truly "stuck" in this orientation, REMD may be
> not useful. I will do a single simulation first at a higher temperature
> (e.g., 400K) in those bad windows to see if the peptide conformations
> are fully sampled.
> 
> Cheers,
> Jianguo
> 
> 
> *From:* Justin A. Lemkul 
> *To:* Gromacs Users' List 
> *Sent:* Wednesday, 23 February 2011 10:24:46
> *Subject:* Re: [gmx-users] Can g_wham support using different
> temperature for different windows?
> 
> 
> 
> Jianguo Li wrote:
>  > Thank you, Justin.
>  > Actually I did windowed umbrella simulations from d=-1.05nm to d=9nm.
> Since I think there is no problem in the region out of the membrane, so
> I only show the configurations within the membrane. My objective is to
> access the free energy barrier of the peptide translocate the negatively
> charged membrane. The problem is that the PMF is not symmetric with
> respect to the bilayer center due to the unconverged simulations.
> 
> I would argue that the PMF is not symmetric because your reaction
> coordinate is not symmetric. How can you calculate a free energy of
> crossing a charged membrane when your peptide does not cross the
> membrane? What I proposed earlier was to obtain configurations at equal
> distances "above" and "below" the membrane (arbitrary in a periodic
> system, but hopefully you get the idea). If you can extract the peptide
> to the point where it is liberated from the membrane in the negative
> direction, I'd suspect you could solve your problem.
> 
>  > Since g_wham does not support different temperatures in different
> windows, to increase the converges, I will probably consider to do REMD
> in those bad windows.
>  >
> 
> This technique might work, provided you don't destabilize the membrane,
> but if the peptide is truly "stuck" in this orientation, I doubt that
> limited-range REMD would be very useful.
> 


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[gmx-users] Residue 'DEF' not found in residue topology database

[Emine Deniz Tekin]

Hi gromacs users,


I am using the gromacs 4.5.3 version. I created a lipopetide which consist
of 12 Carbon atoms (tail) connected to Val-Val-Ala-Gly-Glu-Arg-Gly-Asp
(residues) using ARGUSLAB and I saved it as a pdb file.

Then, when I used the following command in gromacs:

 pdb2gmx   –flipopepArgus.pdb(GROMOS96 45a3 force field&spc
type water model)

 I got the following error message:

 Fatal error:

Residue 'DEF' not found in residue topology database

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors



As far as I could understand, there is no problem with the residues  but  there
is a problem with the atoms in the tail (12 Carbon atoms, 23 Hydrogen atoms
and an Oxygen atom, actually it is called a lauroic acid). These atoms are
defined as DEF.  I thought  I should  rename the pdb to the expected name
given in the .rtp file of  the 45a3 force field for my lipopeptide. But I
could not find a parameterization for the  lauroic acid. In this case, what
shoul I do?


At the
http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blockspage,
I found;


  *Abbrev.*

*Source*

*2*

*Full Name*

*Formula*

*Specifics*

LAU

fa.itp

O

lauroic acid

C11H23COOH

-



Does using fa.itp file solve my problem? If yes, where can I get this file?


I would be so glad if you can help me solve this problem.
Thank you in advance,

Deniz
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Re: [gmx-users] how many contacts has a certain atom at MD

[Justin A. Lemkul]

Olga Ivchenko wrote:
Yes, I want to plot number of contacts agains tempreture. But in 
thermodynamics when temperature changes the pressure changes or the 
volume. But in my system volume and pressure is the same at different 
tempretures. Just I wanted ti be sure if it is ok to do like this even 
if the pressure is the same at different tempretures.




I guess this all depends on how "different" your temperatures are.  If the 
pressures do not change substantially, then there is no problem, since the 
system density is reasonably similar.


-Justin


best,
Olga

2011/2/23 Justin A. Lemkul mailto:jalem...@vt.edu>>



Olga Ivchenko wrote:

If I am using g_mindist to calculate the number of contacts at
different tempretures of the system. I am thinking if it will
make sense because the system has a periodic boundary conditions
and the pressure at each tempreture is defined manually and is
the same. The only parameter in the script which should be
different at different tempretures is pressure. Please could you
advice me on this?


So you want to plot contacts as a function of temperature?  I don't
see any problem with doing that.  On what do you need advice?

-Justin

best,
Olga

2011/2/21 Justin A. Lemkul mailto:jalem...@vt.edu> >>



   Olga Ivchenko wrote:

   So I used mindist for a certain group of molecules which is
   surrounded by water. I got plot number of contacts versuc
   sumulation time. According to what I see in a distance  <
0.6nm
   at certain frame there are on average 150 contacts.

   Actually how the programm calculates the number of
contacts, if
   someone knows what is a creteria that a certain contact
is formed?
   Is is a certain distance.


   Exactly as the title of the output says, a contact exists if
any two
   atoms of the chosen index groups are within 0.6 nm.  You can
change
   the distance with g_mindist -d.

   -Justin

   best,
   Olga

   2011/2/21 Olga Ivchenko mailto:olga.ivche...@gmail.com>
   >


   
   >


   
>
  
   >>

   
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Re: [gmx-users] how many contacts has a certain atom at MD

[Olga Ivchenko]

Yes, I want to plot number of contacts agains tempreture. But in
thermodynamics when temperature changes the pressure changes or the volume.
But in my system volume and pressure is the same at different tempretures.
Just I wanted ti be sure if it is ok to do like this even if the pressure is
the same at different tempretures.

best,
Olga

2011/2/23 Justin A. Lemkul 

>
>
> Olga Ivchenko wrote:
>
>> If I am using g_mindist to calculate the number of contacts at different
>> tempretures of the system. I am thinking if it will make sense because the
>> system has a periodic boundary conditions and the pressure at each
>> tempreture is defined manually and is the same. The only parameter in the
>> script which should be different at different tempretures is pressure.
>> Please could you advice me on this?
>>
>>
> So you want to plot contacts as a function of temperature?  I don't see any
> problem with doing that.  On what do you need advice?
>
> -Justin
>
>  best,
>> Olga
>>
>> 2011/2/21 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>Olga Ivchenko wrote:
>>
>>So I used mindist for a certain group of molecules which is
>>surrounded by water. I got plot number of contacts versuc
>>sumulation time. According to what I see in a distance  < 0.6nm
>>at certain frame there are on average 150 contacts.
>>
>>Actually how the programm calculates the number of contacts, if
>>someone knows what is a creteria that a certain contact is formed?
>>Is is a certain distance.
>>
>>
>>Exactly as the title of the output says, a contact exists if any two
>>atoms of the chosen index groups are within 0.6 nm.  You can change
>>the distance with g_mindist -d.
>>
>>-Justin
>>
>>best,
>>Olga
>>
>>2011/2/21 Olga Ivchenko > >
>>>>
>>
>>
>>   Thank you very much.
>>   best,
>>   Olga
>>
>>   2011/2/21 Justin A. Lemkul > >
>>>>
>>
>>
>>
>>   g_mindist -on (with suitable index groups) should also do
>>the trick.
>>
>>   -Justin
>>
>>
>>   Erik Marklund wrote:
>>
>>   Or g_hbond -contact. Undfortuntely there are still
>> issues
>>   with g_hbond at the moment. Version 4.0.x seem to
>>work better.
>>
>>   XAvier Periole skrev 2011-02-21 11.37:
>>
>>   g_dist
>>   On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote:
>>
>>   Dear Gromacs Users,
>>
>>   I would like to know if there is in gromacs an
>>   option how to calculate how many contacts has a
>>   certain atom i(n a molecules of interest)
>>with water
>>   during the whole MD simulations (or at each
>>step of MD).
>>   Please could you advice me on this?
>>
>>   best,
>>   Olga
>>
>>   -- gmx-users mailing list
>>   gmx-users@gromacs.org 
>>   >>
>>
>>
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>   Please search the archive at
>>
>> http://www.gromacs.org/Support/Mailing_Lists/Search
>>   before posting!
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>>   list. Use the
>>   www interface or send it to
>>   gmx-users-requ...@gromacs.org
>>
>>   >>.
>>
>>   Can't post? Read
>>   http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>>
>>   -- 
>>
>>   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
>>
>>   
>>
>>   -- gmx-users mailing list
>> gmx-users@gromacs.org 
>>   > >>
>>
>>
>>  

Re: [gmx-users] Can g_wham support using different temperature for different windows?

[XAvier Periole]

On Feb 23, 2011, at 3:21 AM, Jianguo Li wrote:



Thank you  for the the useful information, XAvier.
My peptide is highly positively charged, 18 AA with +12 charges.  
Other of my group members told me their NMR experiment in water  
indicates the peptide conformation is very dynamics. Actually I also  
did peptide refolding using REMD in water, and I found it is  
flexible and has no stable structure in water, except some  
instantaneously helical structures. In addition, my peptide consists  
of two branches connected by unnatural peptide bond, so the backbone  
is discontinuous, and also because of the high charges, I assume the  
peptide doesn't form helcial structure in the negatively charged  
membrane. Therefore I didn't put any constraints in the peptide to  
keep the secondary structure of the peptide. I know there are  
assumptions in my model, but I have no other information to increase  
the accuracy of the model.  In fact, when I am doing REMD folding  
simulations using Gromos53a6 and CHARMM27 with cMap, I got different  
results. But the common thing is that both results seems to indicate  
the peptide is filexbile in water without stable secondary  
structure. Then I used MARTINI FF with flexible structure, just to  
find some general features.


I will try your suggestion, doing REMD in those bad windows.

And the reference you mentioned is very useful, I will take a look  
at them :-)


Another question: Suppose some other tools support using different  
temperatures in different windows, as you mentioned, if 500K is too  
high to have a significant contribution to the probability of 300K,   
can I do a series of simulation in a certain window with different  
temparatures (e.g. 300K, 350K, 400K,450K, 500K). In such cases, in  
each window, I need to do 5 simulations, which will be much cheaper  
than doing REMD in that window.
It would be computationally cheaper but this is assuming that you'd  
get the info you are looking for within these simulations and again  
the weight of the conformations from 400/450/500 K at 300 K is  
questionable. Note also that the conformations sampled at high  
temperature with position restrains on the lipids to avoid deformation  
will be difficult to interpret!


Cheers
Jianguo


From: XAvier Periole 
To: Discussion list for GROMACS users 
Sent: Tuesday, 22 February 2011 21:18:12
Subject: Re: [gmx-users] Can g_wham support using different  
temperature for different windows?



A few notes:
- the original method (Kumar-JCC-1992) that inspired wham was actually
developed to mix different temperature simulations. It is however  
not clear

for the type of system you are simulating how much a 500K simulation
would be useful to improve the sampling at 300 K or so. The reason is
that the enthalpy difference between the two systems is so high that  
the
probability that a conformation from a 500K simulation would  
contribute
to sampling at 300K is really low. It would much more efficient for  
systems
with implicit solvent for which the energy of the system does not  
vary so

much with the temperature. One could look at Chodera-JCTC-2007
and ref therein for a few examples.
- I would think that a REMD simulation would be more useful. No need  
to
run 30 replicas to very hight temperature! A bilayer at 500K might  
get funny.


- Martini force field for flexible regions of protein should not be  
trusted ... or
really interpreted with a lot of reserve. The "coil" definition is  
simply something
flexible with absolutely no guaranty that it could be representing  
some thing
even close to reality, which we have only an approximate idea of  
what it is!


- A peptide in a bilayer has a very high chance to get into a  
helical conformation.

Do you think it is reasonable to keep it "flexible"?

- As noted by Justin and Chris, you definitely have a problem of  
convergence ...
I am not sure how many "converged" examples of PMFs of peptide  
crossing a
bilayer are out in the literature (Justin?) but from our experience  
with Martini
it does take an awful lot of time to really get convergence. For you  
system I
would expect at least a microsecond for the windows where sampling  
is an
issue. As an example, we saw significant differences on a PMF  
between two

simple helices up to 8 us ... and no charges were involved.

This might be a lot pessimistic but you should not get fooled by a  
CG model.
Martini is really good for a lot of things but other things should  
really but be

looked at carefully.

XAvier.

On Feb 22, 2011, at 9:12 AM, Jianguo Li wrote:


Sorry I forgot to attach my mdp files.

Here is the mdp file for pulling simulaition:
-




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[gmx-users] test on g_density

[chris . neale]

Could it be this:

http://www.mail-archive.com/gmx-users@gromacs.org/msg35107.html

I've posted a few times on the fact that this tool is broken for  
constant pressure simulations.


I'm not sure why both even and odd would be under the overall average,  
but it seems possible.


Chris.

-- original message --


Hi all.

I've noticed an unexpected behaviour using g_density. I have a
trajectory (with time step 2) and it is split into two subsets (using
trjconv) with, lets say, even and odd steps respectively. According
the the algorithm I expected that the density obtained with the
original trajectory would be the average of the density with each
generated trajectory. However, that was not the case, and for each
slice, while density calculated from the subsets was practically the
same, the density calculated with the original was different (greater
or lower). My system is a membrane, the original trajectory is 50ns
long (25001 steps) and I calculate the density along the bilayer
normal (z). I am using GROMACS4.5.3 and a I've issued the following
commands:

*To get the subsets:
trjconv -f bilayer.xtc -s bilayer.trp -o bilayer_odd -dt 4
trjconv -f bilayer.xtc -s bilayer.trp -o bilayer_even -dt 4 -b 2

The generated trajectories have 12501 and 12500 steps respectively.

*To calculate the densities:
g_density -f bilayer.xtc -s bilayer.tpr -o dens_all
g_density -f bilayer_odd.xtc -s bilayer.tpr -o dens_odd
g_density -f bilayer_even.xtc -s bilayer.tpr -o dens_even

The result is attached. dens_odd and dens_even are very similar, but
surprisingly (at least for me), dens_all is different (it actually
integrates more atoms than the other two).

I haven't seen anything in the code that could explain that result
(maybe when removing pbc??). Is it a bug or a mistake from me?

Thank you!

Javier
-- next part --


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Re: [gmx-users] %exist hydrogen bond

[Justin A. Lemkul]

leila karami wrote:

Dear Justin

yes, I deleted my previous "summary_HBmap.dat" before running the modified 
script.



Send me your input files (.ndx, .pdb, .xpm) off-list and I will have a look. 
Removing the "SOL" conditional is the only thing preventing water H-bonds from 
being considered.  The exact fix that I gave you worked for someone else a while 
back, so I don't know why it's not working for you.


-Justin



--

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group




--


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] Van der waals interaction between nanotubes

[Justin A. Lemkul]

sakthi kumaran wrote:



On Wed, Feb 23, 2011 at 5:25 PM, Justin A. Lemkul > wrote:




sakthi kumaran wrote:

Dear all,
Hi I am new to gromacs. I want to calculate the Van der
waals interaction between two capped CNT facing each other using
the pairwise LJ potential.I haven't used gromacs already. Any
know-how/procedures to do the requiste would be very
helpful.Whether Any tutorials are available for such a kind of
thing...
 



Running a simulation while setting proper energygrps to decompose
short-range nonbonded interactions sounds to be what you need to do.

-Justin


 Thank you in advance guys
 



-- 



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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_sorry I am not getting that. Please explain_


When you run the simulation, set the energygrps keyword in your .mdp file so 
that you have each of your groups of interest specified.  The nonbonded 
potential will be decomposed and the short-range LJ and Coulombic interactions 
are written to the .edr file pairwise for each group, i.e.:


energygrps = A B

will give you energy terms for A-A, A-B, and B-B interactions.

Beyond that, please consult basic tutorial material, the carbon nanotube how-to 
on the Gromacs site, and the extensive discussions of these systems in the list 
archive.


-Justin

--


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] Van der waals interaction between nanotubes

[sakthi kumaran]

On Wed, Feb 23, 2011 at 5:25 PM, Justin A. Lemkul  wrote:

>
>
> sakthi kumaran wrote:
>
>> Dear all,
>> Hi I am new to gromacs. I want to calculate the Van der waals
>> interaction between two capped CNT facing each other using the pairwise LJ
>> potential.I haven't used gromacs already. Any know-how/procedures to do the
>> requiste would be very helpful.Whether Any tutorials are available for such
>> a kind of thing...
>>
>>
>
> Running a simulation while setting proper energygrps to decompose
> short-range nonbonded interactions sounds to be what you need to do.
>
> -Justin
>
>
>   Thank you in advance guys
>>
>>
>
> --
> 
>
> 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
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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*sorry I am not getting that. Please explain*
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[gmx-users] %exist hydrogen bond

[leila karami]

Dear Justin

yes, I deleted my previous "summary_HBmap.dat" before running the
modified script.


-- 

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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Re: [gmx-users] how many contacts has a certain atom at MD

[Justin A. Lemkul]

Olga Ivchenko wrote:
If I am using g_mindist to calculate the number of contacts at different 
tempretures of the system. I am thinking if it will make sense because 
the system has a periodic boundary conditions and the pressure at each 
tempreture is defined manually and is the same. The only parameter in 
the script which should be different at different tempretures is 
pressure. Please could you advice me on this?




So you want to plot contacts as a function of temperature?  I don't see any 
problem with doing that.  On what do you need advice?


-Justin


best,
Olga

2011/2/21 Justin A. Lemkul mailto:jalem...@vt.edu>>



Olga Ivchenko wrote:

So I used mindist for a certain group of molecules which is
surrounded by water. I got plot number of contacts versuc
sumulation time. According to what I see in a distance  < 0.6nm
at certain frame there are on average 150 contacts.

Actually how the programm calculates the number of contacts, if
someone knows what is a creteria that a certain contact is formed?
Is is a certain distance.


Exactly as the title of the output says, a contact exists if any two
atoms of the chosen index groups are within 0.6 nm.  You can change
the distance with g_mindist -d.

-Justin

best,
Olga

2011/2/21 Olga Ivchenko mailto:olga.ivche...@gmail.com> >>


   Thank you very much.
   best,
   Olga

   2011/2/21 Justin A. Lemkul mailto:jalem...@vt.edu> >>



   g_mindist -on (with suitable index groups) should also do
the trick.

   -Justin


   Erik Marklund wrote:

   Or g_hbond -contact. Undfortuntely there are still issues
   with g_hbond at the moment. Version 4.0.x seem to
work better.

   XAvier Periole skrev 2011-02-21 11.37:

   g_dist
   On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote:

   Dear Gromacs Users,

   I would like to know if there is in gromacs an
   option how to calculate how many contacts has a
   certain atom i(n a molecules of interest)
with water
   during the whole MD simulations (or at each
step of MD).
   Please could you advice me on this?

   best,
   Olga

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   -- 

   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] Library file ffamber_tip3p.gro not found in current directory

[Justin A. Lemkul]

sunita gupta wrote:

Hello Everyone

I am setting up a system for protein ligand complex using amber force 
filed with Gromacs 4.5.

in pdb2gmx command i used -water tip3p
but when executing genbox command with -cs ffamber_tip3p.groI am 
getting follwing error "*Fatal error:
Library file in current dir nor  not found ffamber_tip3p.groin default 
directories.

(You can set the directories to search with the GMXLIB path variable)*

Also I manually edited the complex.top file tip3p.itp -> 
ffamber_tip3p.itp...still the problem persists
I searched the /gromacs-4.5/share/gromacs/top directory, and did not 
find any such file there...
Can anyone please guide me where I can get ffamber_tip3p.gro file or 
solve my problem?




There has been significant reorganization to the force field directories in 
Gromacs 4.5.  You can use any 3-point water box to do the solvation, i.e. 
spc216.gro, since AFAIK no other 3-point water coordinate files are distributed 
with Gromacs.  The call to "ffamber_tip3p.itp" is also outdated.  Look into the 
new force field structure to get the proper call for your force field (i.e. 
amberXX.ff/tip3p.itp).


-Justin



--
--
SUNITA GUPTA



--


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] %exist hydrogen bond

[Justin A. Lemkul]

leila karami wrote:

Dear Justin

thanks for your reply.

I did what you said as follows:

your main script=

# Open up the structure file and work with it
print "Processing coordinate file...\n";
foreach $_ (@coord) {
 my @line = split(" ", $_);
 my $natom = $line[1];
 my $name = $line[2];
 my $resn = $line[3];
 my $resnum = $line[4];
151
152 if ($line[0] =~ /ATOM/) {
153 unless ($resn =~ /SOL/) {
154 for (my $z=1; $z<=$nres; $z++) {
155 if ($donors{$z} == $natom) {
156 $donor_names[$z] = $name;
157 $donor_resn[$z] = join('', $resn, $resnum);
158 } elsif ($acceptors{$z} == $natom) {
159 $acceptor_names[$z] = $name;
160 $acceptor_resn[$z] = join('', $resn, $resnum);
161  }
 }
 }
 }
}
 
# open a single output file for writing


 
my modified script=


# Open up the structure file and work with it
print "Processing coordinate file...\n";
foreach $_ (@coord) {
 my @line = split(" ", $_);
 my $natom = $line[1];
 my $name = $line[2];
 my $resn = $line[3];
 my $resnum = $line[4];
 
 if ($line[0] =~ /ATOM/) {

  for (my $z=1; $z<=$nres; $z++) {
 if ($donors{$z} == $natom) {
 $donor_names[$z] = $name;
 $donor_resn[$z] = join('', $resn, $resnum);
 } elsif ($acceptors{$z} == $natom) {
 $acceptor_names[$z] = $name;
 $acceptor_resn[$z] = join('', $resn, $resnum);
}
 }
 }
}
 
# open a single output file for writing


is my manner true?
when I used modified script, problem was not solved. and output file is 
as follows:




Did you delete your previous "summary_HBmap.dat" before running the script 
again?  Output will be appended rather than overwritten.


-Justin


#DonorAcceptor% Exist.
 0.160
  NGL1 N0.400
 ARG58   NH243.565
 ARG58   NH2 1.839
 ARG58   NH1 0.080
 ARG58   NH1 21.663
 ARG58   NH1 0.160
 ARG58NE  1.359
. 
.

.
.
  GLY3 O 1.759
  GLY4 O 0.400
 THR47 O61.711
 ASN51   OD116.867
 ASN51   ND2 0.320
GLN23   OE111.191
.
.
.

how to fix it?
--

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group




--


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] Van der waals interaction between nanotubes

[Justin A. Lemkul]

sakthi kumaran wrote:

Dear all,
 Hi I am new to gromacs. I want to calculate the Van der waals 
interaction between two capped CNT facing each other using the pairwise 
LJ potential.I haven't used gromacs already. Any know-how/procedures to 
do the requiste would be very helpful.Whether Any tutorials are 
available for such a kind of thing...
 


Running a simulation while setting proper energygrps to decompose short-range 
nonbonded interactions sounds to be what you need to do.


-Justin

 
Thank you in advance guys
 



--


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] Re: Adding chromophore parameters to the charmm force field

[Justin A. Lemkul]

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

If you have specific implementation questions based on this information, post 
those.  Right now, your question is too broad for anyone to invest the 
significant amount of time it would take to walk you through the whole process.


-Justin

bharat gupta wrote:

Hi,

I have obtained the chromophore parameters of the GFP for charmm force 
field but I am not able to find it out how to add it to the charmm FF 
file.. I have two files one is the topology file , which looks like this :- 


*
   221
MASS13 CP2c   12.01100 C ! his CE1 carbon
MASS14 NR2c   14.00700 N ! neutral his unprotonated ring nitrogen
MASS15 NR1c   14.00700 N ! neutral his protonated ring nitrogen
MASS16 CP1c   12.01100 C ! his CG and CD2 carbons
MASS17 Och15.99900 O ! carbonyl oxygen
MASS18 CE1c   12.01100 C ! for alkene; RHC=CR
MASS19 HA1c1.00800 H ! for alkene; RHC=CR
MASS41 CA412.01100 C ! aromatic C
MASS42 HPc 1.00800 H ! aromatic H
MASS43 OHc15.99900 O ! from OH1
MASS44 Hch 1.00800 H ! polar H
MASS45 CT3c   12.01100 C ! aliphatic sp3 C for CH3
MASS46 HAc 1.00800 H ! nonpolar H
MASS47 CA112.01100 C ! aromatic C
MASS48 CA212.01100 C ! aromatic C
MASS49 CA312.01100 C ! aromatic C

DECL -CA
DECL -C
DECL -O
DECL +N
DECL +HN
DECL +CA
DEFA FIRS NTER LAST CTER
AUTO ANGLES DIHE


AUTOGENERATE ANGLES DIHE
DEFA FIRS NONE LAST NONE

RESI CRO  0.000
GROUP   ! Imidazolinone ring
ATOM C1 CP2c  0.76
ATOM N2 NR2c -0.55
ATOM N3 NR1c -0.64
ATOM C2 CP1c  0.80
ATOM O2 Och  -0.61
ATOM CA CP1c  0.24
!
GROUP   ! Charges from propene
ATOM CB CE1c -0.10
ATOM HB HA1c  0.10
!
GROUP   ! Tyr ring : charges from charmm22
ATOM CG2 CA1   0.00
ATOM CD1 CA2  -0.115
ATOM HD1 HPc   0.115
ATOM CD2 CA2  -0.115
ATOM HD2 HPc   0.115
ATOM CE1 CA3  -0.115
ATOM HE1 HPc   0.115
ATOM CE2 CA3  -0.115
ATOM HE2 HPc   0.115
ATOM CZ CA40.11
ATOM OH Ohc   -0.54
ATOM HH Hch0.43
!
!Glycine part / C=O taken from Charmm22
GROUP
ATOM CAg  CT2-0.18  ! |
ATOM HA1  HB  0.09  ! |
ATOM HA2  HB  0.09  ! HA1-CA-HA2
GROUP   ! |
ATOM CC   0.51  ! |
ATOM OO  -0.51  ! C=O
!
!Serine part / taken from Charmm22
GROUP
ATOM NNH1-0.47  ! |
ATOM HN   H   0.31  !  HN-N
ATOM CAs  CT1 0.07  ! |   HB1
ATOM HA   HB  0.09  ! |   |
GROUP   !  HA-CA--CB--OG
ATOM CBs  CT2 0.05  ! |   | \
ATOM HB1  HA  0.09  ! |   HB2HG1
ATOM HB2  HA  0.09  !   O=C
ATOM OG1  OH1-0.66  ! |
ATOM HG1  H   0.43

 



Other file is the parameter file :-

! GFP Chromophore parameters, protonated form
!
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb  b0
CA1  CA2   305.00  1.3750 !
CA2  CA3   305.00  1.3750 !
CA3  CA4   305.00  1.3750 !
HPc  CA1   340.000 1.08   !
HPc  CA2   340.000 1.08   !
HPc  CA3   340.000 1.08   !
HPc  CA4   340.000 1.08   !
Ohc  Hch   545 0.96   ! 
Ohc  CA4   334.3   1.4110 !
HA1c CE1c  360.500 1.10   ! 
NR1c CP1c  400.000 1.41   !
NR1c CP2c  400.000 1.39   ! 
NR2c CP2c  400.000 1.30   ! 
NR2c CP1c  400.000 1.40   !

CP1c CP1c  410.000 1.49   !
CP1c CE1c  560 1.36   !
CP1c Och   807 1.22   !
CE1c CA1   370 1.45   !
NR1c CT2   352 1.45   ! 
CP2c CT1   320 1.49   ! 



ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types KthetaTheta0   Kub S0
!
NR2c CP2c NR1c  130.00114.00   ! 
CP2c NR2c CP1c  130.00106.00   ! 
CP2c NR1c CP1c  130.00107.90   ! 
NR2c CP1c CP1c  130.00108.30   ! 
NR2c CP1c CE1c   45.80129.50   ! 
NR1c CP1c OcH42.00126.00   !
NR1c CP1c CP1c  130.00103.00   ! 
OcH  CP1c CP1c   38.00132.00   !
CP1c CP1c CE1c   45.80122.00   ! 
CP1c CE1c CA1   130.00130.00   ! 
CP1c CE1c HA1c   42.00114.00   ! 
CE1c CA1  CA245.80 121.00   
HA1c CE1c CA142.00 116.00   ! 
CA1  CA2  CA3   40.000120.00   35.00   2.41620

CA2  CA1  CA2   40.000120.00   35.00   2.41620
CA2  CA3  CA4   40.000120.00   35.00   2.41620
CA3  CA4  CA3   40.000120.00   35.00   2.41620
!
HPc  CA3  CA4   30.000120.00   22.00   2.15250 
HPc  CA3  CA2   30.000120.00   22.00   2.15250

HPc  CA2  CA3   30.000120.00   22.00   2.15250
HPc  CA2  CA1   30.000120.00   22.00   2.15250
!
Ohc  CA4  CA3   45.200   120. ! ALLOW   ARO ALC
HcH  Ohc  CA4   65.000   108. ! ALLOW   ALC ARO
!
!Connection to the ser fragment
!--
CT2  CT1  CP2c52.000   108. ! ALLOW   ALI PEP POL ARO
HB   CT1  CP2c  50.000   109.5000 ! ALLOW  PEP
NH1  CT1  CP2c  50.000   107. ! ALLOW   

Re: [gmx-users] Can g_wham support using different temperature for different windows?

[Patrick Fuchs]

Hi,
I think your PMF is asymetric because your peptide is asymetric and you 
don't sample enough. To get a symetric PMF, your peptide would have to 
sample all the possible conformations *and* orientations in each window. 
Thus it means that for the windows in the center of the bilayer (where 
you say it's extended and interacts with the two monolayers) it'll have 
to rotate completely the other way round. This event will probably be 
*very* rare because you have to translocate positive charges across the 
membrane which cost ~ 40 to 50 kJ/mol (see the PMF of Lys+ and Arg+ in 
10.1021/ct700324x).
So as suggested by Chris, Justin and Xavier, you'll have to sample way 
more than 100 ns per window. I think you should go at least to the 
microsecond time scale (or more?). Or maybe starting from different 
initial conformations/orientations for a given window and then 
concatenate the different trajectories?
Also consider the remark of Xavier, TM or interfacial peptides are most 
of the time alpha-helical within the membrane. So far in literature, 
PMFs of a whole peptide across a bilayer were done by restraining the 
peptide in a helical conformation (e.g. 10.1016/j.bpj.2010.12.3682). It 
is anyway a very difficult problem (and probably impossible at atomistic 
resolution) to get a converged PMF for a whole peptide (e.g. 
10.1016/j.bpj.2009.03.059).

Ciao,

Patrick

Le 23/02/2011 05:25, Jianguo Li a écrit :

Sorry, why do you think the PMF should be asymmetric?

I pulled my peptide from d=9nm (above the membrane) to d=-3nm (below the
membrane) and I did windowed umbrella sampling in the range of d=-1.05nm
to d=9nm. At least the PMF should be symmetric with respect of the
bilayer center in the range of d=[-1.05nm 1.05nm], something like a
guassian distribution. But I got asymmetric PMF in this region. I also
did reverse pulling starting from the peptide below the membrane ending
with the peptide above the membrane. And the subsequent PMF of reversed
pulling is also asymmetic.

I have position restrains of the phosphate beads of the lipids in
z-direction. So the membrane should be stable in REMD. But as you
mentioned, if peptide is truly "stuck" in this orientation, REMD may be
not useful. I will do a single simulation first at a higher temperature
(e.g., 400K) in those bad windows to see if the peptide conformations
are fully sampled.

Cheers,
Jianguo


*From:* Justin A. Lemkul 
*To:* Gromacs Users' List 
*Sent:* Wednesday, 23 February 2011 10:24:46
*Subject:* Re: [gmx-users] Can g_wham support using different
temperature for different windows?



Jianguo Li wrote:
 > Thank you, Justin.
 > Actually I did windowed umbrella simulations from d=-1.05nm to d=9nm.
Since I think there is no problem in the region out of the membrane, so
I only show the configurations within the membrane. My objective is to
access the free energy barrier of the peptide translocate the negatively
charged membrane. The problem is that the PMF is not symmetric with
respect to the bilayer center due to the unconverged simulations.

I would argue that the PMF is not symmetric because your reaction
coordinate is not symmetric. How can you calculate a free energy of
crossing a charged membrane when your peptide does not cross the
membrane? What I proposed earlier was to obtain configurations at equal
distances "above" and "below" the membrane (arbitrary in a periodic
system, but hopefully you get the idea). If you can extract the peptide
to the point where it is liberated from the membrane in the negative
direction, I'd suspect you could solve your problem.

 > Since g_wham does not support different temperatures in different
windows, to increase the converges, I will probably consider to do REMD
in those bad windows.
 >

This technique might work, provided you don't destabilize the membrane,
but if the peptide is truly "stuck" in this orientation, I doubt that
limited-range REMD would be very useful.

-Justin

 > Cheers
 > Jianguo
 >
 > 
 > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
 > *To:* Gromacs Users' List mailto:gmx-users@gromacs.org>>
 > *Sent:* Tuesday, 22 February 2011 21:10:08
 > *Subject:* Re: [gmx-users] Can g_wham support using different
temperature for different windows?
 >
 >
 >
 > Jianguo Li wrote:
 > > Thanks Justin and Chris and sorry for confusing interpretation.
 > > Let me make it more clear. My peptide is flexible Martini beads,
and highly positively charged. My membrane is a mixture of negatively
charged lipids (25%) and zitterionic lipids(75%). So there is strong
electrostatic attraction
 > > between peptide and membrane. To get the PMF, I did the following:
 > >
 > > (1) I did pulling simulation along (0 0 -1) direction to pull my
peptide across the membrane. Then I got different configurations
corresponding to different windows along the reaction coordinates, which
is

Re: [gmx-users] scaling of replica exchange

[Mark Abraham]

On 02/23/11, Fabio Affinito   wrote:
> Hi Mark,
> I've checked with Valeria and the problem is actually on the setup of
> the system (unfair overlapping of the temperature distribution). So I
> think that the loss of efficiency should be of a factor between 2 or 3
> in her case and not more.
> 

That's going to affect the usefulness of doing replica-exchange, but not the 
computational performance when doing it. Doing exchanges that never/always 
succeed makes essentially no difference to the performance.

Mark


> On 02/23/2011 10:31 AM, Mark Abraham wrote:
> > 
> > 
> > On 02/23/11, *Valeria Losasso *  wrote:
> >>
> >> Thank you Mark. I found one message of this month concerning this
> >> topic, and there are some small suggestions. I don't think that such a
> >> changes can restore a factor of 26, but it could be worth to try to
> >> see what happens. I will let you know.
> > 
> > They won't. The problem is that every 10 (or so) MD steps every
> > processor does global communication to check nothing's gone wrong. That
> > resulted from some unrelated bits of code trying to share the same
> > machinery for efficiency, and treading on each others' toes.
> > 
> > Mark
> > 
> >> Valeria
> >>
> >>
> >>
> >> On Wed, 23 Feb 2011, Mark Abraham wrote:
> >>
> >> >
> >> >
> >> >On 02/23/11, Valeria Losasso  wrote:
> >> >
> >> >  Dear all,
> >> >  I am making some tests to start using replica exchange
> >> molecular dynamics on my system in water. The setup is ok
> >> >  (i.e. one replica alone runs correctly), but I am not able to
> >> parallelize the REMD. Details follow:
> >> >
> >> >  - the test is on 8 temperatures, so 8 replicas
> >> >  - Gromacs version 4.5.3
> >> >  - One replica alone, in 30 minutes with 256 processors, makes
> >> 52500 steps. 8 replicas with 256x8 = 2048
> >> >  processors, make 300 (!!) steps each = 2400 in total (I arrived
> >> to these numbers just to see some update of the
> >> >  log file: since I am running on a big cluster, I can not use
> >> more than half an hour for tests with less than 512
> >> >  processors)
> >> >  - I am using mpirun with options -np 256 -s  md_.tpr -multi 8
> >> -replex 1000
> >> >
> >> >
> >> >There have been two threads on this topic in the last month or so,
> >> please check the archives. The implementation of
> >> >multi-simulations scales poorly. The scaling of replica-exchange
> >> itself is not great either. I have a working version under
> >> >final development that scales much better. Watch this space.
> >> >
> >> >Mark
> >> >
> 
> 
> -- 
> *
> Fabio Affinito, PhD
> CINECA
> SuperComputing Applications and Innovation Department - SCAI
> Via Magnanelli, 6/3
> 40033 Casalecchio di Reno (Bologna) ITALY
> +39/051/6171794 (Phone)
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Re: [gmx-users] scaling of replica exchange

[Fabio Affinito]

Hi Mark,
I've checked with Valeria and the problem is actually on the setup of
the system (unfair overlapping of the temperature distribution). So I
think that the loss of efficiency should be of a factor between 2 or 3
in her case and not more.

Bye,

Fabio

On 02/23/2011 10:31 AM, Mark Abraham wrote:
> 
> 
> On 02/23/11, *Valeria Losasso *  wrote:
>>
>> Thank you Mark. I found one message of this month concerning this
>> topic, and there are some small suggestions. I don't think that such a
>> changes can restore a factor of 26, but it could be worth to try to
>> see what happens. I will let you know.
> 
> They won't. The problem is that every 10 (or so) MD steps every
> processor does global communication to check nothing's gone wrong. That
> resulted from some unrelated bits of code trying to share the same
> machinery for efficiency, and treading on each others' toes.
> 
> Mark
> 
>> Valeria
>>
>>
>>
>> On Wed, 23 Feb 2011, Mark Abraham wrote:
>>
>> >
>> >
>> >On 02/23/11, Valeria Losasso  wrote:
>> >
>> >  Dear all,
>> >  I am making some tests to start using replica exchange
>> molecular dynamics on my system in water. The setup is ok
>> >  (i.e. one replica alone runs correctly), but I am not able to
>> parallelize the REMD. Details follow:
>> >
>> >  - the test is on 8 temperatures, so 8 replicas
>> >  - Gromacs version 4.5.3
>> >  - One replica alone, in 30 minutes with 256 processors, makes
>> 52500 steps. 8 replicas with 256x8 = 2048
>> >  processors, make 300 (!!) steps each = 2400 in total (I arrived
>> to these numbers just to see some update of the
>> >  log file: since I am running on a big cluster, I can not use
>> more than half an hour for tests with less than 512
>> >  processors)
>> >  - I am using mpirun with options -np 256 -s  md_.tpr -multi 8
>> -replex 1000
>> >
>> >
>> >There have been two threads on this topic in the last month or so,
>> please check the archives. The implementation of
>> >multi-simulations scales poorly. The scaling of replica-exchange
>> itself is not great either. I have a working version under
>> >final development that scales much better. Watch this space.
>> >
>> >Mark
>> >


-- 
*
Fabio Affinito, PhD
CINECA
SuperComputing Applications and Innovation Department - SCAI
Via Magnanelli, 6/3
40033 Casalecchio di Reno (Bologna) ITALY
+39/051/6171794 (Phone)
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Re: [gmx-users] scaling of replica exchange

[Mark Abraham]

On 02/23/11, Valeria Losasso   wrote:
> 
> Thank you Mark. I found one message of this month concerning this topic, and 
> there are some small suggestions. I don't think that such a changes can 
> restore a factor of 26, but it could be worth to try to see what happens. I 
> will let you know.
> 

They won't. The problem is that every 10 (or so) MD steps every processor does 
global communication to check nothing's gone wrong. That resulted from some 
unrelated bits of code trying to share the same machinery for efficiency, and 
treading on each others' toes.

Mark


> Valeria
> 
> 
> 
> On Wed, 23 Feb 2011, Mark Abraham wrote:
> 
> >
> >
> >On 02/23/11, Valeria Losasso  wrote:
> >
> >  Dear all,
> >  I am making some tests to start using replica exchange molecular 
> >dynamics on my system in water. The setup is ok
> >  (i.e. one replica alone runs correctly), but I am not able to 
> >parallelize the REMD. Details follow:
> >
> >  - the test is on 8 temperatures, so 8 replicas
> >  - Gromacs version 4.5.3
> >  - One replica alone, in 30 minutes with 256 processors, makes 52500 
> >steps. 8 replicas with 256x8 = 2048
> >  processors, make 300 (!!) steps each = 2400 in total (I arrived to 
> >these numbers just to see some update of the
> >  log file: since I am running on a big cluster, I can not use more than 
> >half an hour for tests with less than 512
> >  processors)
> >  - I am using mpirun with options -np 256 -s  md_.tpr -multi 8 -replex 
> >1000
> >
> >
> >There have been two threads on this topic in the last month or so, please 
> >check the archives. The implementation of
> >multi-simulations scales poorly. The scaling of replica-exchange itself is 
> >not great either. I have a working version under
> >final development that scales much better. Watch this space.
> >
> >Mark
> >
>
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Re: [gmx-users] how many contacts has a certain atom at MD

[Olga Ivchenko]

If I am using g_mindist to calculate the number of contacts at different
tempretures of the system. I am thinking if it will make sense because the
system has a periodic boundary conditions and the pressure at each
tempreture is defined manually and is the same. The only parameter in the
script which should be different at different tempretures is pressure.
Please could you advice me on this?

best,
Olga

2011/2/21 Justin A. Lemkul 

>
>
> Olga Ivchenko wrote:
>
>> So I used mindist for a certain group of molecules which is surrounded by
>> water. I got plot number of contacts versuc sumulation time. According to
>> what I see in a distance  < 0.6nm at certain frame there are on average 150
>> contacts.
>>
>> Actually how the programm calculates the number of contacts, if someone
>> knows what is a creteria that a certain contact is formed?
>> Is is a certain distance.
>>
>>
> Exactly as the title of the output says, a contact exists if any two atoms
> of the chosen index groups are within 0.6 nm.  You can change the distance
> with g_mindist -d.
>
> -Justin
>
>  best,
>> Olga
>>
>> 2011/2/21 Olga Ivchenko > olga.ivche...@gmail.com>>
>>
>>
>>Thank you very much.
>>best,
>>Olga
>>
>>2011/2/21 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>g_mindist -on (with suitable index groups) should also do the
>> trick.
>>
>>-Justin
>>
>>
>>Erik Marklund wrote:
>>
>>Or g_hbond -contact. Undfortuntely there are still issues
>>with g_hbond at the moment. Version 4.0.x seem to work better.
>>
>>XAvier Periole skrev 2011-02-21 11.37:
>>
>>g_dist
>>On Feb 21, 2011, at 11:32 AM, Olga Ivchenko wrote:
>>
>>Dear Gromacs Users,
>>
>>I would like to know if there is in gromacs an
>>option how to calculate how many contacts has a
>>certain atom i(n a molecules of interest) with water
>>during the whole MD simulations (or at each step of
>> MD).
>>Please could you advice me on this?
>>
>>best,
>>Olga
>>
>>-- gmx-users mailing list
>> gmx-users@gromacs.org
>>
>>
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>>.
>>
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>>
>>
>>
>>
>>
>>-- 
>>
>>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
>>
>>
>>
>>-- gmx-users mailing listgmx-users@gromacs.org
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>>
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>>
>>
>>
>>
> --
> 
>
> 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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w

Re: [gmx-users] GROMACS installation query

[Carsten Kutzner]

On Feb 23, 2011, at 6:16 AM, Tom Dupree wrote:

> Greetings all,
>  
> I am new to Linux and wish to confirm  some facts before I press on with the 
> installation.
>  
> In the installation guide, 
> http://www.gromacs.org/Downloads/Installation_Instructions
> There is a line saying  “...Where assembly loops are in use, GROMACS 
> performance is largely independent of the compiler used. However the GCC 
> 4.1.x series of compilers are broken for GROMACS, and these are provided with 
> some commodity Linux clusters. Do not use these compilers!...”
>  
> Firstly I assume this still applies to GROMACS version 4.5 and not just to 
> earlier ones. (Confirm/deny?)
To my knowledge there are no workarounds for gcc 4.1.x compiler bugs in the 
newer Gromacs
versions. 

> Secondly I read this as GCC 4.2.x and greater should be fine. (confirm/deny?)
Yes. You could also use the Intel compiler which will typically give you one or 
two percent
extra performance. But do not expect too much.

Carsten
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[gmx-users] Library file ffamber_tip3p.gro not found in current directory

[sunita gupta]

Hello Everyone

I am setting up a system for protein ligand complex using amber force filed
with Gromacs 4.5.
in pdb2gmx command i used -water tip3p
but when executing genbox command with -cs ffamber_tip3p.groI am getting
follwing error "*Fatal error:
Library file in current dir nor  not found ffamber_tip3p.groin default
directories.
(You can set the directories to search with the GMXLIB path variable)*

Also I manually edited the complex.top file tip3p.itp ->
ffamber_tip3p.itp...still the problem persists
I searched the /gromacs-4.5/share/gromacs/top directory, and did not find
any such file there...
Can anyone please guide me where I can get ffamber_tip3p.gro file or solve
my problem?


-- 
-- 
SUNITA GUPTA
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[gmx-users] %exist hydrogen bond

[leila karami]

Dear Justin

thanks for your reply.

I did what you said as follows:

your main script=

# Open up the structure file and work with it
print "Processing coordinate file...\n";
foreach $_ (@coord) {
 my @line = split(" ", $_);
 my $natom = $line[1];
 my $name = $line[2];
 my $resn = $line[3];
 my $resnum = $line[4];
151
152 if ($line[0] =~ /ATOM/) {
153 unless ($resn =~ /SOL/) {
154 for (my $z=1; $z<=$nres; $z++) {
155 if ($donors{$z} == $natom) {
156 $donor_names[$z] = $name;
157 $donor_resn[$z] = join('', $resn, $resnum);
158 } elsif ($acceptors{$z} == $natom) {
159 $acceptor_names[$z] = $name;
160 $acceptor_resn[$z] = join('', $resn, $resnum);
161  }
 }
 }
 }
}

# open a single output file for writing


my modified script=

# Open up the structure file and work with it
print "Processing coordinate file...\n";
foreach $_ (@coord) {
 my @line = split(" ", $_);
 my $natom = $line[1];
 my $name = $line[2];
 my $resn = $line[3];
 my $resnum = $line[4];

 if ($line[0] =~ /ATOM/) {
  for (my $z=1; $z<=$nres; $z++) {
 if ($donors{$z} == $natom) {
 $donor_names[$z] = $name;
 $donor_resn[$z] = join('', $resn, $resnum);
 } elsif ($acceptors{$z} == $natom) {
 $acceptor_names[$z] = $name;
 $acceptor_resn[$z] = join('', $resn, $resnum);
}
 }
 }
}

# open a single output file for writing

is my manner true?
when I used modified script, problem was not solved. and output file is as
follows:

#DonorAcceptor% Exist.
 0.160
  NGL1 N0.400
 ARG58   NH243.565
 ARG58   NH2 1.839
 ARG58   NH1 0.080
 ARG58   NH1 21.663
 ARG58   NH1 0.160
 ARG58NE  1.359
.
.
.
.
  GLY3 O 1.759
  GLY4 O 0.400
 THR47 O61.711
 ASN51   OD116.867
 ASN51   ND2 0.320
GLN23   OE111.191
.
.
.

how to fix it?
-- 

Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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[gmx-users] GROMACS installation query

[Tom Dupree]

Greetings all,

I am new to Linux and wish to confirm  some facts before I press on with the 
installation.

In the installation guide, 
http://www.gromacs.org/Downloads/Installation_Instructions
There is a line saying  "...Where assembly loops are in use, GROMACS 
performance is largely independent of the compiler used. However the GCC 4.1.x 
series of compilers are broken for GROMACS, and these are provided with some 
commodity Linux clusters. Do not use these compilers!..."

Firstly I assume this still applies to GROMACS version 4.5 and not just to 
earlier ones. (Confirm/deny?)
Secondly I read this as GCC 4.2.x and greater should be fine. (confirm/deny?)

Thank you for your time,

Tom
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Re: [gmx-users] scaling of replica exchange

[Valeria Losasso]

Thank you Mark. I found one message of this month concerning this topic, 
and there are some small suggestions. I don't think that such a changes 
can restore a factor of 26, but it could be worth to try to see what 
happens. I will let you know.


Valeria



On Wed, 23 Feb 2011, Mark Abraham wrote:




On 02/23/11, Valeria Losasso  wrote:

  Dear all,
  I am making some tests to start using replica exchange molecular dynamics 
on my system in water. The setup is ok
  (i.e. one replica alone runs correctly), but I am not able to parallelize 
the REMD. Details follow:

  - the test is on 8 temperatures, so 8 replicas
  - Gromacs version 4.5.3
  - One replica alone, in 30 minutes with 256 processors, makes 52500 
steps. 8 replicas with 256x8 = 2048
  processors, make 300 (!!) steps each = 2400 in total (I arrived to these 
numbers just to see some update of the
  log file: since I am running on a big cluster, I can not use more than 
half an hour for tests with less than 512
  processors)
  - I am using mpirun with options -np 256 -s  md_.tpr -multi 8 -replex 1000


There have been two threads on this topic in the last month or so, please check 
the archives. The implementation of
multi-simulations scales poorly. The scaling of replica-exchange itself is not 
great either. I have a working version under
final development that scales much better. Watch this space.

Mark
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Re: [gmx-users] scaling of replica exchange

[Valeria Losasso]

Sorry Luca, my mistake in writing. I used actually 2048.
Valeria



On Wed, 23 Feb 2011, Luca wrote:


Hi Valeria,

Dear all,
I am making some tests to start using replica exchange molecular dynamics
on my system in water. The setup is ok (i.e. one replica alone runs
correctly), but I am not able to parallelize the REMD. Details follow:

- the test is on 8 temperatures, so 8 replicas
- Gromacs version 4.5.3
- One replica alone, in 30 minutes with 256 processors, makes 52500 steps.
8 replicas with 256x8 = 2048 processors, make 300 (!!) steps each = 2400
in total (I arrived to these numbers just to see some update of the log
file: since I am running on a big cluster, I can not use more than half an
hour for tests with less than 512 processors)
- I am using mpirun with options -np 256 -s  md_.tpr -multi 8 -replex 1000

I think that with this option you are  using 256/8=32 cpu for each replica.
If you want use 256 for each replica you cna try set up -np option
equal to 256x8 = 2048.

Luca


Do you have any idea?
Thanks in advance

Valeria



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