[gmx-users] Re:problem with simulation of freezing of water
Hi, Also note that it is difficult to simulate the right structure of ice (Ih). You didn't write what you want to study, but search the literature carefully. You may need to use an ab-initio model. Ran Message: 7 Date: Sun, 11 Nov 2012 11:26:19 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Re:problem with simulation of freezing of water To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 509fd1ab.50...@vt.edu Content-Type: text/plain; charset=UTF-8; format=flowed On 11/11/12 11:22 AM, Ali Alizadeh wrote: Dear Justin Thank you for reply, I want to simulation of water freezing, my condition: pressure=300 bar and T=240 k , number 1656, run time= 100ns, I can not see regular structure of ice by MD simulation or by gromacs? In your opinion, if i want this structure of ice for my simulation, What can i do? Start by searching the literature for a suitable protocol. Ice simulations have been done before. As I said before, each water model has a different melting point, and hardly any of them correspond to the actual experimental value. See if you can produce a suitable simulation with a pressure of 1 bar (proof of concept) and then change conditions. What you have to keep in mind is that most water models were designed to work at ambient conditions for normal simulations. They do not necessarily work under extremes or produce useful results under those conditions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! End of gmx-users Digest, Vol 103, Issue 52 ** -- gmx-users mailing listgmx-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! * Please don't post (un)subscribe requests to the 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
[gmx-users] Re: genion problem with divalent ions
Hi, As a side note, you should be careful when using Mg (and probably all other multiply charged ions, as well as large polarisable ions like I-). It's very difficult to correctly represent the interactions of such ions in the bulk correctly using non-polarisable force fields. Ran Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden Norrgård, room 328d http://lnu.se/ccbg On 9 September 2012 16:10, gmx-users-requ...@gromacs.org wrote: Message: 2 Date: Sun, 9 Sep 2012 13:53:35 +0200 From: Matthias Ernst un...@student.kit.edu Subject: [gmx-users] genion problem with divalent ions To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 504c833f.2050...@student.kit.edu Content-Type: text/plain; charset=ISO-8859-15; format=flowed Hi, I just encountered (another) strange thing with genion. I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp: 2, forcefield amber99sb), so I expected half of the system charge (-52) to be added as ions. BUT it added the same amount, i.e. 52 Mg ions instead of 26 which would be needed for neutralization. The same holds for Zn or Ca ions, which also are divalent in ions.itp Could it be that the routines of genion to determine the number of ions are not working properly? I mean, the -neutral option also does work only if the -conc flag is also there and provides a value 0.0 (which in fact is not what I want when I just want do neutralize my system by adding ions...) Does anyone of you also had similar problems? Thank you, Matthias -- gmx-users mailing listgmx-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! * Please don't post (un)subscribe requests to the 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
[gmx-users] RE: quasi-harmonic entropy calculation
Hi, IIRC I tested g_anaeig when David wrote it and the results were the same as calc_entropies.pl, so it sounds strange. Are you sure you use the same input in both cases? Did you use the eigenvectors that correspond to the same eigenvalues? Also, how may eigenvalues are close to zero? Ran Message: 4 Date: Thu, 22 Mar 2012 10:27:36 -0400 From: wmira...@estudiantes.fbio.uh.cu Subject: [gmx-users] Re: quasi-harmonic entropy calculation To: gmx-users@gromacs.org Message-ID: 5e667c140e0c268c9e87681be3535b89.squir...@est.fbio.uh.cu Content-Type: text/plain;charset=iso-8859-1 My name is Williams. I am a Biochemistry student. I have done QH entropy calculation using g_anaeig, but I found an old perl script at GROMACS web site to do the same. The problem is that when I calculate entropy for the loops of my protein the results are the same using g_anaeig or the old perl script, but when I compare the entropy calculated through both methods for my entire protein the results diverges in one order of magnitud and I give to the script the same eigenvalues obtained by g_covar (g_anaeig uses the eigenvectors). Please, help me. Thanks -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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
[gmx-users] RE: g_clustsize
Dear Stefano, I forward your question to the gromacs-users mailing list. Please send further inquiries there - there may be people more qualified than me to reply (unless you refer to my modified version or to one of my papers) I'm not sure if the .xpm files give the information you're interested at but using g_clustsize -av and -hc is useful to get the average size and distribution. You can further use -mcn and extract the index group of the largest cluster. By a combination of scripting and other Gromacs tools you can get more info on the largest cluster per frame if you need it. g_clustsize doesn't give you the radius of gyration of the cluster. My modified version does, but only for the largest cluster - not for all as you need I guess. Good luck, Ran Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden Norrgård, room 328d +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/ccbg From: Stefano [boro...@unitus.it] Sent: 26 July 2011 15:49 To: Ran Friedman Subject: Dear Prof Friedman I am Stefano Borocci, a GROMACS user. I am currently studying, through molecular dynamics simulations, the self-assembly of Gemini surfactants. I have some problems to use the g_clustsize of GROMACS and I don't understand the results obtained with this tool. I have analyzed the xtc file of my trajectory g_clustsize -f trj.xtc -s top.tpr -mol (and without) -cut 0.35 and the cluster size and cluster distributions predicted by g_clustsize does not match with what I see by a visual analysis of trajectory (using VMD). I also tried to remove the periodic boundary (-pbc mol) without result. I have two questions: How to calculate the cluster (micelle) size and cluster distribution of my sistem? How to calculate the radius of gyration of the aggregates if in my box there are more clusters (3 or 4)? I would be very grateful if you could help me Thanks in advance. Best regards Stefano Borocci -- --- Dr Stefano Borocci Laboratorio di Chimica e Chimica Computazionale Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF) Università degli Studi della Tuscia Largo dell'Università, snc 01100 Viterbo Tel. +39-0761-357127 +39-0761-357193 Fax +39 0761-357179 e-mail: boro...@unitus.it --- -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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
[gmx-users] RE: Including quadrupole-charge interaction in GROMACS (WU Yanbin)
Hi,
Not implemented in Gromacs AFAIK.
Note that (1) even the definition of a quadruple isn't straightforwards and
depends on the orientation and (2) common FF parameters were not developed with
higher ordered multiple taken into account.
@Article{Plattner2009,
author = Plattner, N and Meuwly, M,
title = {Higher order multipole moments for molecular dynamics simulations},
journal = J Mol Model,
year = 2009,
volume = 15,
pages = 687-694
}
Ran
Ran Friedman
Biträdande Lektor (Assistant Professor)
Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden
Norrgård, room 328d
+46 480 446 290 Telephone
+46 76 207 8763 Mobile
ran.fried...@lnu.se
http://lnu.se/ccbg
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Today's Topics:
1. Re: CHARMM forcefield (Justin A. Lemkul)
2. Re: local pressure calcuation for Gromacs-4.5 (Justin A. Lemkul)
3. Including quadrupole-charge interaction in GROMACS (WU Yanbin)
4. g_density (chris.ne...@utoronto.ca)
5. Position restraints (Tom Dupree)
6. Re: Position restraints (Mark Abraham)
--
Message: 1
Date: Wed, 15 Jun 2011 17:11:08 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] CHARMM forcefield
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4df91fec.8080...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
simon sham wrote:
Hi,
I have two questions about using the charmm force field.
1. Do we still need to use the two perl scripts, convert_charmm_
to_gromacs.pl and fix_top_for_charmm.pl?
No.
2. I got the following note when I tried to do energy minim. with grompp:
NOTE 1 [file topol.top]:
The largest charge group contains 12 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
Is this a problem?
Yes. CHARMM topologies should not use charge groups. You should invoke pdb2gmx
with the -nochargegrp option to create a proper topology.
-Justin
Thanks for your insight!
Simon
--
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
--
Message: 2
Date: Wed, 15 Jun 2011 17:17:53 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] local pressure calcuation for Gromacs-4.5
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4df92181.2090...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Amit Choubey wrote:
Dear all,
Could anyone direct me to the manual for local pressure calculation or a
place where everything is mentioned about it ? I have been only able to
collect bits and pieces from the mailing lists.
That's probably all there is to be found. There's no manual linked from the git
web interface or the ftp site.
-Justin
Thank you
Amit
On Wed, Jun 15, 2011 at 5:35 AM, Mark Abraham mark.abra...@anu.edu.au
mailto:mark.abra...@anu.edu.au wrote:
On 15/06/2011 9:09 PM, Jianguo Li wrote:
Dear all,
I have made a test calculation of local pressure using version 4.5
for my membrane simulation using CHARMM FF. When rerun the
simulation, mdrun gives the localpressure data. Howeve, instead of
giving an anveraged data of the local pressure, mdrun gives a
separate file for each frame, so I got many files:
localpressure.dat0, localpressure.dat1, localpressure.dat2,
localpressure.dat3 ..
Then I need to calculate the pressure tensor for each frame and
make average. but these localpressure.dat files are very big (each
file is about 30 Mb), occupying large space of the hard disk. Can
[gmx-users] RE: Essential dynamics - concepts (Kavyashree M)
From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Essential dynamics - concepts To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTim7wkRbvJZiJJbuHg=mkp5dgfu...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Kavya, Its g_covar contributed by Dr. Rossen apostolov if I am right.? Here it states that those which are having correlation coefficient better than 0.5 will be reported, so covariance gives those which have correlation coefficient less than 0.5? I don't know the modified version. But I presume that the components with eigenvalues higher than 0.5 are written out, which is not quite the same as having a correlation coefficient of 0.5. It's the correlation coefficient indeed. the version is available from the Gromacs user contributions site. Ran -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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
[gmx-users] RE: Metal surfaces (Sergio Manzetti)
Hi,
That's unlikely, but maybe the following publications can help you to build the
surface:
@Article{Iori2008,
author = Iori, F and Corni, S,
title = {Including image charge effects in the molecular dynamics simulations
of molecules on metal surfaces},
journal = J Comput Chem,
year = 2008,
volume = 29,
pages = 1656-1666
}
@Article{Iori2009,
author = Iori, F and Di Felice, R and Molinari, E and Corni, S,
title = {{G}ol{P}: {A}n atomistic force-field to describe the interaction of
proteins with {A}u(111) surfaces in water},
journal = J Comput Chem,
year = 2009,
volume = 30,
pages = 1465-1476
}
@article{Kalcher2009,
Author = {Kalcher, I. and Horinek, D. and Netz, R. R. and Dzubiella, J.},
Title = {{Ion specific correlations in bulk and at biointerfaces}},
Journal = {JOURNAL OF PHYSICS-CONDENSED MATTER},
Year = {{2009}},
Volume = {{21}},
Article-Number = {{424108}}
}
Ran Friedman
Biträdande Lektor (Assistant Professor)
Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden
Norrgård, room 328d
+46 480 446 290 Telephone
+46 76 207 8763 Mobile
ran.fried...@lnu.se
http://lnu.se/ccbg
Hello, does anybody have an idea if there are availbale PDB files which
represent metal surfaces for transition state metals, to be used for MD?
BW
S
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[gmx-users] RE: micelles and trjconv -pbc cluste
Hi, I've sent the program off list. I hope to have a version compatible with the current or future version of Gromacs and will then upload it to the user contributions. Ran -- Message: 2 Date: Thu, 14 Apr 2011 13:29:42 -0700 (PDT) From: jim jack blhaw...@yahoo.com Subject: [gmx-users] Re: micelles and trjconv -pbc cluster To: gmx-users@gromacs.org Message-ID: 401162.89007...@web35301.mail.mud.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Dear Ran Friedman and Tsjerk Wassennaar, ? ?First of all, thanks to all responses to my problem. As far as the modified versions of g_clustsize and trjconv, I really want to try them.??Best regards? George Koros -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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
[gmx-users] RE: micelles and trjconv -pbc cluster
Hi, Likewise, I have a modified version of g_clustsize that calculates the radius of gyration for the largest structure and can send you the code. Ran Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden Norrgård, room 328d +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/ccbg Message: 4 Date: Thu, 14 Apr 2011 17:44:07 +0200 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] micelles and trjconv -pbc cluster To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: BANLkTin-YV43F=s1r-ng8xnzj9ejeqr...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi George, Recently I wrote an alternative, non-iterative clustering routine, that does not suffer from convergence failures. If you want, I can send you the modified trjconv source code. Note that it does not bother about the center of mass of the cluster, but just builds a network of neighbours, until there are no more. If you're clusters are not periodic, it won't matter. Let me know... Cheers, Tsjerk On Thu, Apr 14, 2011 at 4:48 PM, Erik Marklund er...@xray.bmc.uu.se wrote: jim jack skrev 2011-04-14 16.42: Dear GROMACS users, I am trying to simulate an SDS micelle in water. As simulation time goes by, the micelle approaches the edge of the box and consequently some of these molecules get in from the other side. This leads to incorrect radius of gyration, eccentricity, etc. A solution to this problem is the option trjconv -pbc cluster as described in the page http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering. In this case, the problem is that it takes a lot of time and a huge file (several GB) is created due to this procedure. Is there any other alternative? Thanks in advance George Koros I don't think that the cluster option always converges. You could, if your micelle is intact at frame 0, first do trjconv -pbc nojump, then optionally trjconv -center. That should give a trajectory from which you could calculate the radius of gyration. If SDS molecules occationally leave the micelle and recombine with a priodic, then you might have a problem with the suggested approach. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755er...@xray.bmc.uu.se http://folding.bmc.uu.se/ -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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 -- 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 -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110414/2adc27d7/attachment.html -- -- 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! End of gmx-users Digest, Vol 84, Issue 120 ** -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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
[gmx-users] RE: Regarding DCCM analysis with g_covar available in user contributed section
Hi, As stated below the upper half of the triangle shows correlations having r0.5 or r-0.5, that is |r|0.5 Ran From: bipin singh [bipinel...@gmail.com] Sent: 12 March 2011 12:27 To: Discussion list for GROMACS users Cc: r.fried...@bioc.uzh.ch Subject: Regarding DCCM analysis with g_covar available in user contributed section Hello, I am using g_covar vailable in user contributed section (by Ran Friedman) the description available for the package is as follows: This package contains a modified version of g_covar, which can print a matrix of atomic correlation coefficients (with -xpmc) and write all pairs with a correlation 0.5 to a log file (with -clog). Otherwise it is the same as the original program. The xpm correlation matrix shows only cross-correlations larger than 0.5 (absolute values) on the upper triangle and all values on the lower triangle. Thus, the upper triangle displays only the most correlated motions. As stated that the upper triangle only shows the cross-correlation greater than 0.5, but I am also getting some negative correlation values(blue regions) in above triangle. I don't know what is the region behind this. Plz help me to understand this behaviour. I have attached my xpm matrix file generated using g_covar. -- - Thanks and regards Bipin Singh -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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
[gmx-users] Re: RE: simulation of a metal binding sites (bharat gupta)
Hi,
If you know the structure of the zinc binding domain and assume that the zinc
ion stays in place it may be all right to use the bonded representation.
Recent publications:
@article{Lin2010,
author = {Lin, F and Wang, R},
title = {Systematic Derivation of {AMBER} Force Field Parameters Applicable to
Zinc-Containing Systems},
journal = {J Chem Theory Comput},
volume = {6},
pages = {1852-1870},
year = {2010}
}
@Article{Peters2010,
author = Peters, M B and Yang, Y and Wang, B and F{\u}sti-Moln{\'a}r, L and
Weaver, M N and Merz, K M,
title = {Structural Survey of Zinc Containing Proteins and the Development of
the Zinc {AMBER} Force Field ({ZAFF})},
journal = J Chem Theory Comput,
year = 2010,
volume = 6,
pages = 2935-2947
}
You have to know quite a lot on the structure to use this approach.
Good luck,
Ran.
Ran Friedman
Biträdande Lektor (Assistant Professor)
Linnaeus University
School of Natural Sciences
391 82 Kalmar, Sweden
Norrgård, room 328d
+46 480 446 290 Telephone
+46 76 207 8763 Mobile
ran.fried...@lnu.se
http://lnu.se/ccbg
Message: 6
Date: Thu, 17 Feb 2011 23:46:02 -0800
From: bharat gupta bharat.85.m...@gmail.com
Subject: Re: [gmx-users] RE: simulation of a metal binding sites
To: Discussion list for GROMACS users gmx-users@gromacs.org,
baa...@smplinux.de
Message-ID:
AANLkTi=7rJZLS6B+hQvjNH5Su=qf3y9ay75ebm9fh...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Thanks for these two references ... I am trying to simulate a zinc ion
(Zn++) binding domains .. Actually the study involves grafting the Zinc ion
domain onto some other protein to check whether it binds to ions or not and
what will be the effect of ion binding onto the topology of the other
protein to which the zinc ion binding domain is attached .
On Thu, Feb 17, 2011 at 11:15 PM, Marc Baaden baa...@smplinux.de wrote:
Hi,
As mentioned by others, there's really lots of literature out there. I
thought I mention a recent study we carried out, because it actually
helped discover some new ion binding sites based on MD. By re-examining
crystal structures based on these results, we could even find
experimental evidence for those ions being there. [1]
But actually you didn't tell us which ions you want to simulate?
Monovalent ions should be sort of ok, although there are differences
among the forcefields (some original KCl used to crystallize).
Di-valent ions, in particular Ca2+, are much more tricky. Higher
charged ones are a nightmare. The higher the charge, the more likely
you might want things like polarization in your simulation.
There are also some specific forcefields finely parameterized for ions
based on quantum mechanics. I suggest you check out SIBFA [2] by Gresh
and Piquemal.
Good luck,
Marc
[1] How Cations Can Assist DNase I in DNA Binding and Hydrolysis
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001000
[2] SIBFA (Sum of Interactions Between Fragments Ab initio computed)
http://www.lct.jussieu.fr/pagesperso/jpp/SIBFA.html
bharat.85.m...@gmail.com said:
Thankx for the reply ...
Can you refer some papers which can be helpful for me to do MD
simulation of proteins with ions ... It will be of great help.. I
searched the gromacs user list but couldn't get much material..
--
Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr
FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
--
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--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
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[gmx-users] RE: simulation of a metal binding sites
Hi, There are methodological difficulties in simulating multivalent ions together with proteins. Check the mailing list for a discussion and reference. This is not an issue of Gromacs but of dealing with protein-ion interactions using a classical non-polarisable force field. Check the literature. Ran. Message: 3 Date: Wed, 16 Feb 2011 20:14:07 -0800 From: bharat gupta bharat.85.m...@gmail.com Subject: [gmx-users] RE: simulation of a metal binding sites To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: aanlktin06ut6+wrfpz4a79fq9g-galmk35uxecph+...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, I have incorporated some metal binding sites(zinc ion) in my protein. Now I want to see whether that region binds to zinc ions or not and what is the effect of ion binding to the topology of the protein .. Can this be done using gromacs and how ?? Regards -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/c1c1ccc7/attachment-0001.html -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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
Re: [gmx-users] Simulation using Martini force field
Hi Regina, Most CG force fields for proteins are less versatile than all-atom force fields and are simply not adequate for every application. As the secondary structure is determined a priori, you cannot model secondary structure changes, as probably happen during aggregation - even if the definition of the unordered protein was correct. You probably need to choose another FF or method. The UNRES FF from the Scheraga group doesn't suffer from this limitation, but isn't implemented in Gromacs and may have other caveats. You can take a look at the MARTINI web page and paper (on the protein FF) about the definition of secondary structure. Best regards, Ran Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden Norrgård, room 328d +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/ccbg -- Message: 1 Date: Tue, 15 Feb 2011 00:43:51 +0200 From: pol...@fh.huji.ac.il Subject: Re: [gmx-users] Simulation using Martini force field To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 20110215004351.13575htmiyeiz...@webmail.huji.ac.il Content-Type: text/plain; charset=UTF-8; DelSp=Yes;format=flowed Thank you very much for you reply. Can you please explain me why do i need secondary structure file at all and why secondary structure is pre-defined and thus static throughout a simulation? I didn't see that something like this defined for lipids. How do I use do_dssp to build the needed file? I saw that I need a topology file in rder to use do_dssp. Where can I find this topology file? I hope this is ok that I'm asking so many questions. Thank you very much for your help. Regina Quoting XAvier Periole x.peri...@rug.nl: Dear Regina, You have two problems: 1- the parameterization of phosphorylated serine should be done following the same philosophy of Martini. Check the Martini papers to see how this is done. In short partitioning is of primary importance. 2- you want to simulate unfolded protein ... indeed there is evidently no persistent structure in such system and therefore the choice for secondary structure would be coil in the Martini force field. However the definition of coil for Martini has not been parameterize to reproduce anything even close to what an unfolded protein, assuming that we know what it looks like :)) The Martini coil is simply something flexible. I am afraid Martini is just not ready for simulating unfolded proteins. Any outcome of a simulation would have to be interpreted with CARE! XAvier. On Feb 14, 2011, at 2:09 PM, pol...@fh.huji.ac.il wrote: Dear Gromacs users and developers, I'm interested to run simulation of natively unstructured protein (casein), that can self assembly and create micelles, using Martini force field. The initial structure of the monomer was created and minimized using Sybyl. This protein includes also 4 phosporylated serines. I'm trying to understand how should I set my system. I started from the tutorial (http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-water) but I found that have no idea how to create a phosphorylated serine inCG structure (I have it in my initial pdb). In addition, I found that I need a secondary structure of the protein and I don't have something like this. Moreover, this protein doesn't have one. I will appreciated very much if somebody can help me and guide me a little. Thank you very much in advance. Regina -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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
RE: [gmx-users] .psf and .dcd files
Hi, You can use wordom to convert .xtc files to .dcd. As for the .psf AFAIK you'll have to work on it yourself using CHARMM or psfgen. Ran Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden Norrgård, room 328d +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of atila petrosian [atila.petros...@gmail.com] Sent: 19 December 2010 11:04 To: gmx-users@gromacs.org Subject: [gmx-users] .psf and .dcd files Dear gromacs users I did simulation of protein-ligand by gromacs 4.0.7 with amber 03 forcefield. I need to .psf and .dcd files. can I convert/obtain them? any help will highly appreciated. -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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
RE: [gmx-users] .psf and .dcd files
Hi, psfgen is a part of VMD but maybe you can also use it separately. Note that you have to give it the right input and parameters, and I don't know if it works with AMBER-FF. Good luck Ran From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of atila petrosian [atila.petros...@gmail.com] Sent: 19 December 2010 12:36 To: gmx-users@gromacs.org Subject: [gmx-users] .psf and .dcd files Dear Ran thanks for your reply. Is psfgen a separately program? -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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
RE: [gmx-users] proton proton transfer
Hi Olga, It's not straightforward in CHARMM as well. One method is to use conjugate peak refinement, but this will only get you the potential energy surface, but there's also a force field made by Meuwly for dealing with proton transfer IIRC. Depending on the system size, you may want to use QM/MM (implemented in Gromacs) or simulate your system with a DFT-based 'on semi-empricial code. Ran Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden Norrgård, room 328d +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Olga Ivchenko [olga.ivche...@gmail.com] Sent: 02 December 2010 14:59 To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] proton proton transfer Thnaks, Justin. Probably CHARMM is suitable for this. 2010/12/2 Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu Olga Ivchenko wrote: Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I read about umbrella sampling, but may be there is other techniques? You can't do this with standard MD. Bonds cannot break and re-form in a classical force field. You might be able to do accomplish it with QM, however, but in that case you need to be looking outside of Gromacs. -Justin Yours sincerely, Olga -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.orgmailto: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! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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
RE: [gmx-users] proton proton transfer
Sorry for the typo below. DFT based *or* semi empirical code. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Ran Friedman Sent: 02 December 2010 15:01 To: Discussion list for GROMACS users Subject: RE: [gmx-users] proton proton transfer Hi Olga, It's not straightforward in CHARMM as well. One method is to use conjugate peak refinement, but this will only get you the potential energy surface, but there's also a force field made by Meuwly for dealing with proton transfer IIRC. Depending on the system size, you may want to use QM/MM (implemented in Gromacs) or simulate your system with a DFT-based 'on semi-empricial code. Ran Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden Norrgård, room 328d +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Olga Ivchenko [olga.ivche...@gmail.com] Sent: 02 December 2010 14:59 To: jalem...@vt.edu; Discussion list for GROMACS users Subject: Re: [gmx-users] proton proton transfer Thnaks, Justin. Probably CHARMM is suitable for this. 2010/12/2 Justin A. Lemkul jalem...@vt.edumailto:jalem...@vt.edu Olga Ivchenko wrote: Dear gromacs users, I want to simulate proton transfer between water and another small molecule in gromacs. In the end I should have the velosity of proton proton exchange. Please can you advice me which method is better to use for this in gromacs. I read about umbrella sampling, but may be there is other techniques? You can't do this with standard MD. Bonds cannot break and re-form in a classical force field. You might be able to do accomplish it with QM, however, but in that case you need to be looking outside of Gromacs. -Justin Yours sincerely, Olga -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.eduhttp://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.orgmailto: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! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.orgmailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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 -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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
RE: [gmx-users] Claculating Equilibrium constants
Hi Gideon, If the binding is relatively weak and the force field parameters are good enough that should be feasible. See e.g., Biophys J. 2005 August; 89(2): 768–781. However, in other cases this is more challenging. This is discussed in details for simulations of a Zinc binding protein in Phys Chem Chem Phys. 2009 Feb 14; 11(6): 975-83 Good luck, Ran Ran Friedman Biträdande Lektor (Assistant Professor) Linnaeus University School of Natural Sciences 391 82 Kalmar, Sweden +46 480 446 290 Telephone +46 76 207 8763 Mobile ran.fried...@lnu.se http://lnu.se/research-groups/computational-chemistry-and-biochemistry-group?l=en From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of גדעון לפידות [glapid...@gmail.com] Sent: 30 November 2010 10:45 To: gmx-users@gromacs.org Subject: [gmx-users] Claculating Equilibrium constants Hello all, I have a protein bound to ions. is there a way to calculate the Kd of the bound ion in Gromaces so I can compare it to experimental Kd? Thanks, Gideon -- gmx-users mailing listgmx-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! Please don't post (un)subscribe requests to the 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
Re: [gmx-users] RE: Targeted MD
Hi, -r and -rb are for FEP. If you want to bias your simulation's sampling, you can use the pull code, essential dynamics sampling or flooding, all of which are described in the manual and literature. Ran Nimesh Jain wrote: Hello, I realize that this topic has been discussed before, but I just need to ascertain a few things: I have a system of about 1400 atoms with implicit solvent and I want to do a targeted MD. While doing the pre-processing, if I just specify grompp -r in.gro -rb out.gro, is this sufficient or are there any other things that I need to consider. Also, I have tabulated potentials. If any one knows how to do this, or if you need more info on my system, please let me know. Thanks, Nimesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Is there a way to calculate the hydrodynamic radius using GROMACS?
Hi Art, For a globular protein, it should correlate with the gyration radius. You can have a look at Dashevskaya et al., PROTOPLASMA 234: 13-23 for some discussion about the relation of the radius of gyration and Stokes radius. Ran Berk Hess wrote: Hi, There might be a way to do this with Gromacs. But I would think a protein is simply a volume (maybe with one attached water layer) for which there is a simple approximation for the hydrodynamic radius in hydrodynamics. Berk From: aroberts99...@yahoo.com To: gmx-users@gromacs.org Date: Wed, 18 Aug 2010 14:25:26 -0700 Subject: [gmx-users] Is there a way to calculate the hydrodynamic radius using GROMACS? Hi, all, I was curious, if there is a way to calculate the hydrodynamic radius of a protein using GROMACS? Much appreciated, Art Dr. Arthur Roberts, Ph.D. University of California, San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences 9500 Gilman Drive #0703 La Jolla, CA 92093-0703 email: aroberts99...@yahoo.com cell: 206-850-7468 skype=aroberts92122 -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Entropy from NMA
Hi, Can you post the exact commands you used for EM and NMA? Ran nahren manuel wrote: Dear Gromacs Users, I am trying to calculate Entropy from Normal Mode Analysis. I minimized the structure to 8.41750710592449e-09 Then I calculated the normal mode (the mdp file is given below). But when i try to calculate the Eigenvalues, I get the following warning One of the lowest 6 eigenvalues has a non-zero value. This could mean that the reference structure was not properly energy minimized. Writing eigenvalues... I get only negative eigenvalues. Let me also add that I used the same mdp file for minimization changing the integrator to steep, cg and finally to l-bfgs. Best, nahren --- integrator= nm constraints = none define = -DFLEXIBLE emtol= 0.0001 emstep = 0.0001 nsteps= 5 nstlist= 1 ns_type= grid rlist= 1.5 coulombtype= shift rcoulomb-switch= 1.0 rvdw-switch= 1.0 vdwtype = shift rcoulomb = 1.3 rvdw = 1.3 -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Entropy from NMA
p.s. How big is this negative value? Ran Friedman wrote: Hi, Can you post the exact commands you used for EM and NMA? Ran nahren manuel wrote: Dear Gromacs Users, I am trying to calculate Entropy from Normal Mode Analysis. I minimized the structure to 8.41750710592449e-09 Then I calculated the normal mode (the mdp file is given below). But when i try to calculate the Eigenvalues, I get the following warning One of the lowest 6 eigenvalues has a non-zero value. This could mean that the reference structure was not properly energy minimized. Writing eigenvalues... I get only negative eigenvalues. Let me also add that I used the same mdp file for minimization changing the integrator to steep, cg and finally to l-bfgs. Best, nahren --- integrator= nm constraints = none define = -DFLEXIBLE emtol= 0.0001 emstep = 0.0001 nsteps= 5 nstlist= 1 ns_type= grid rlist= 1.5 coulombtype= shift rcoulomb-switch= 1.0 rvdw-switch= 1.0 vdwtype = shift rcoulomb = 1.3 rvdw = 1.3 -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Entropy from NMA
Dear Rui, Thanks for the info - maybe it's better to submit a bugzilla for the NMA in parallel then, do I'm not sure if this can be checked on run-time with mdrun. From Nahren's description I understood that multiples files were generated and assumed that they were backups (as if you run identical MD multiple times with the same input and files). Ran J. Rui Rodrigues wrote: Dear Ran and Nahren, I run into a similar problem a couple of weeks ago: http://lists.gromacs.org/pipermail/gmx-users/2010-July/052377.html In short, integrator = steep can be run in parallel. Output from parallel and single-node are equal. integrator = l-bfgs runs only in single-node, as advertised in the manual. mdrun dies with a fatal error if one tries to run in parallel: Fatal error: Cannot do parallel L-BFGS Minimization - yet. integrator = nm runs in parallel without any error. However, output is wrong: mdrun write multiple hessian.mtx files, each with small size. mdrun seems to get in to some kind of race condition, because sometimes only one .mtx is produced (still, with small size). Running g_nmeig in these parallel mtx results in huge all-negative eigenvalues. The same input in single-node goes just fine, with first 6 eigenvalues close to zero. Rui Rodrigues On Wed, 28 Jul 2010 12:55:44 +0200, Ran Friedman wrote Your NMA seem to run on one processor four times. I'm not sure if the EM part can be run in parallel. This doesn't seem to be the reason for the negative eigenvalue. What was the g_anaeig command (with flags)? nahren manuel wrote: Dear Ran, I ran the whole NMA again and I found where I go wrong. I hope it will help others as well. (sorry for a big email) In steps 1 2 (of minimization) I kept the C-alpha frozen. 1. doublegrompp -f em1.mdp -c r1dodecapdb.pdb -p r1top.top -o em1tpr.tpr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em1tpr Steepest Descents converged to Fmax 100 in 2569 steps Potential Energy = -6.21296128286120e+03 Maximum force = 9.87358378592302e+01 on atom 701 Norm of force = 1.04875323563923e+01 2. doublegrompp -f em2.mdp -c em1tpr.gro -p r1top.top -o em2tpr.tpr -t em1tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em2tpr Polak-Ribiere Conjugate Gradients converged to Fmax 1 in 6596 steps Potential Energy = -7.56682084795001e+03 Maximum force = 9.92719787231560e-01 on atom 1320 Norm of force = 6.47772253797808e-02 3. doublegrompp -f em3.mdp -c em2tpr.gro -p r1top.top -o em3tpr.tpr -t em2tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em3tpr Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 writing lowest energy coordinates. Steepest Descents converged to machine precision in 3018 steps, but did not reach the requested Fmax 10. Potential Energy = -8.49398064549505e+03 Maximum force = 6.86336687926682e+01 on atom 935 Norm of force = 7.15798864024085e+00 4. doublegrompp -f em4.mdp -c em3tpr.gro -p r1top.top -o em4tpr.tpr -t em3tpr.trr mpirun -np 8 ~/gmxdpr/bin/doublemdrun -v -deffnm em4tpr Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 0.01 writing lowest energy coordinates. Polak-Ribiere Conjugate Gradients converged to machine precision in 21674 steps, but did not reach the requested Fmax 0.01. Potential Energy = -9.66058047638671e+03 Maximum force = 1.49342602818840e+00 on atom 590 Norm of force = 1.86576579430541e-01 5.doublegrompp -f em5.mdp -c em4tpr.gro -p r1top.top -o em5tpr.tpr -t em4tpr.trr ~/gmxdpr/bin/doublemdrun -v -deffnm em5tpr Low-Memory BFGS Minimizer converged to machine precision in 10346 steps, but did not reach the requested Fmax 0.0001. Potential Energy = -9.66337416273684e+03 Maximum force = 6.48625019025464e-04 on atom 581 Norm of force = 6.35632681200205e-05 6.doublegrompp -f em6.mdp -c em5tpr.gro -p r1top.top -o em6tpr.tpr -t em5tpr.trr Low-Memory BFGS Minimizer converged to machine precision in 3316 steps, but did not reach the requested Fmax 1e-08. Potential Energy = -9.66337416275038e+03 Maximum force = 6.48788529801368e-05 on atom 8 Norm of force = 6.56362137550289e-06 7. doublegrompp -f em7.mdp -c em6tpr.gro -p r1top.top -o em7tpr.tpr -t em6tpr.trr Low-Memory BFGS Minimizer converged to machine precision in 7530 steps, but did not reach the requested Fmax 1e-08. Potential Energy = -9.66337416275071e+03 Maximum force = 4.07762128402886e-07 on atom 10 Norm of force = 5.79534451487287e-08 8. doublegrompp -f em8.mdp -c em7tpr.gro -p r1top.top -o em8tpr.tpr -t em7tpr.trr Low-Memory BFGS Minimizer converged to Fmax 1e-08 in 5840 steps Potential Energy = -9.66337416275070e+03 Maximum force = 8.41750710592449e-09 on atom 521 Norm of force = 1.2888919393e-09 NMA 9
Re: [gmx-users] NPH Simulations
Hi, You can run a simulation with a barostat but with no temperature coupling. It's probably a good idea to make sure that the system is equilibrated in terms of the temperature first (with NPT). Also, I'd use a small timestep and double precision. Search the literature for protocols from researchers who have already employed NPH, though that's not too common. Ran sapna sarupria wrote: Hi All, I was wondering if there is a way to run simulations in the NPH ensemble in Gromacs. Does any one have experience doing this? Thank you Sapna -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_cluster Jarvis-Patrick
Hi, The nearest neighbours are defined according to RMSD between the structures. If M=10, a new conformation x is added to a given cluster when a conformation y in the cluster exists such that: (1) x and y are neighbours, i.e., x has y among the 10 conformations with minimal RMSD to x and vice versa for y. (2) x any y have at least P (default: 3) neighbours in common. You may want to prepare a diagram to graphically illustrate this. Ran Marc Charendoff wrote: Hello, In the Jarvis-Patrick method g_cluster shows that when M=0, the cutoff is used to determine nearest neighbors (those within X.X nm). In the absence of cutoff - e.g. M is defaulted to 10, how are nearest neighbors determined? What does M=10 (or anyother number) mean? Thanks, Marc -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: g_cluster settings
Marc - Note that you used the linkage method which maps a structure to a cluster if its distance to any structure already in the cluster is is less than the cutoff. If you think it's not representative of your system try another clustering method, but note that you may need a longer trajectory as well. Vitali - g_clustersize is for clustering molecules (can be useful e.g., for the formation of micelles) whereas g_cluster is for clustering the trajectories. Ran Vitaly Chaban wrote: Dear Marc: Please look towards g_clustzise (instead of g_cluster). We tried to use g_cluster some years ago and eventually switched to g_clustzise - I do not remember why but the latter was more successful. If you want to monitor the number of clusters in the system, g_clustzise can certainly do it. Dr. Vitaly Chaban I am trying to perform a cluster analysis on a 4 ns trajectory (4000 frame trajectory), but I am not getting any more than 1 cluster until I get down to a cutoff of 0.05 nm. This seems like an awfully small number, so I checked my rmsd distribution and found that 44% of my rmsds are at 0.1 nm or greater. My distribution looks like the following: And my command line is as follows: g_cluster -f md.trr -s md.tpr -n index.ndx -sz clustersize1.xvg -clid clusterid1.xvg -cutoff .10 -cl clusters1.pdb -b 1 -e 4001 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Electric field, potential, dielectric constant
Hi, You may want to use a Poisson-Boltzmann solver, e.g., APBS for this purpose. Ran Vladimir Lankevich wrote: Dear Gromacs Users, I have several questions about electrostatics in Gromacs. I am simulating two proteins in water, separated by certain distance, and was interested in their electrostatic interactions. I was wondering if Gromacs can calculate and show me values of electric field or electric potential at any point within the volume. If yes, how can this be done? I looked through the manual and did not find much. I tried using g_potential, but it only gives me ten values for electric field (if I use 10 slices, and particular direction). This confused me, because I thought that in the system each coordinate would have different electric field. How should I interpret the results of g_potential? Also, can I use Gromacs to compute dielectric constant of a particular region within the volume? How can I do that? Thank you very much!! Cheers, Vladimir -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] large forces and monstrous water molecules in energy minimization step
Hi, For the dynamics to work you indeed need smaller forces (on the order of 10^3 in GMX units). Using flexible water molecules I was able to get this for your NaCl model. Just add: define = -DFLEXIBLE To your input. This should work also to fill in the voids I guess. Ran -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- Justin A. Lemkul wrote: Use a different box size. I replicated your problem, but your run completes successfully with a box set up with editconf -d 1 instead of -d 3.3. If you set nstxout = 1 during the EM process, you'll see the problematic water molecule become unstable. It looks as if there is a small void in the solvent (due to the way genbox tries to stack solvent configurations) and your water molecule simply can't find a good orientation within that void. -Justin Ehud Schreiber wrote: Dear GROMACS users, When trying to simulate a pair of interacting proteins in water, I have encountered problems that ultimately resulted in the simulation crashing. I then tried to simplify the system as far as possible while retaining the problem; I now believe the problem (or at least a part of it) lies in the energy minimization step (the first molecular dynamics one). Specifically, the forces encountered during this step are very large, and some water molecules (which are supposed to be rigid) become giant and misshapen. In more details: 1) I use GROMACS version 4.0.7, single precision, on a server with two Intel x86-64 processors and the redhat 5.4 linux OS. 2) I created a PDB file, called NaCl.pdb, with only two “atoms”, actually Na+ and Cl- ions separated by their distance in the lattice of salt: HET NA A 1 1 HET CL A 1 1 HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 1 NANA 1+ FORMUL 2 CLCL 1- HETATM1 NANA A 1 -1.410.0 0.01.00 0.0 NA HETATM2 CLCL A 1 +1.410.0 0.01.00 0.0 CL 3) I use the tip3p water model: pdb2gmx -f NaCl.pdb -water tip3p 4) I create the box: editconf -f conf.gro -bt dodecahedron -d 3.3 -o box.gro 5) I add water using spc216, creating the saltwater.gro file (which seems O.K. by inspection): genbox -cp box.gro -cs spc216.gro -p topol.top -o saltwater.gro 6) I create the energy minimization parameter file em.mdp: --em.mdp-- integrator = steep nsteps = 200 nstlist = 10 rlist = 1.0 coulombtype = pme rcoulomb= 1.0 vdwtype = Cut-off rvdw= 1.0 nstenergy = 10 -- 7) I prepare the em.tpr file for the energy minimization run: grompp -f em.mdp -p topol.top -c saltwater.gro -o em.tpr 8) I run the energy minimization step: mdrun -v -deffnm em 9) Looking at the em.log file I see that this step converged to machine precision but did not have maximal force 10: … Enabling SPC water optimization for 7561 molecules. … Max number of connections per atom is 2 Total number of connections is 30244 Max number of graph edges per atom is 2 Total number of graph edges is 30244 Going to use C-settle (7561 waters) wo = 0.33, wh =0.33, wohh = 3, rc = 0.075695, ra = 0.0390588 rb = 0.0195294, rc2 = 0.15139, rone = 1, dHH = 0.15139, dOH = 0.09572 … Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax 10 … Steepest Descents converged to machine precision in 36 steps, but did not reach the requested Fmax 10. Potential Energy = -3.4678925e+05 Maximum force = 6.4623531e+05 on atom 11052 Norm of force = 5.4643726e+03 10) Looking at the em.gro file I see one monstrous water molecule (no. 3686); e.g., it has |HW2-OW| = 3.384876 nm, while the normal distance is about 0.1 nm. Its HW2 atom (no. 11054) is close to another water molecule (no. 5849), e.g., 0.047 nm from the latter’s HW2 atom (no. 17543): … 3686SOL OW11052 4.348 3.778 -0.629 3686SOLHW111053 5.360 2.601 0.505 3686SOLHW211054 6.518 1.650 0.861 … 5849SOL OW17541 6.525 1.698 0.900 5849SOLHW117542 6.606 1.649 0.918 5849SOLHW217543 6.481 1.648 0.832 … 11) During the simulation, several files called stepnnl.pdb were produced for problematic steps, where nn=11,15,19 and l=b,c. For example, the file step19c.pdb indeed shows a problematic water molecule no. 3686, while step19b.pdb does not. Likewise, the earlier step11c.pdb shows
Re: [gmx-users] Re: Simulation with CsCl
Dear Sonali,
Unfortunately development of force-field parameters is difficult, and
even more so for bivalent ions and transition metals. This is certainly
not suitable as a project to begin with.
Having said that, a careful search in the literature will reveal that
many sets of parameters for metal ions do exist. Try to find a set that
works best with the water model that you're using or your particular
model, and carry out some simulations to validate that the results are
correct, reproducible and robust. The following references discuss some
aspects of simulations of ions and proteins:
@article{Project2006,
Author = {Project, E. and Friedman, R. and Nachliel, E. and Gutman, M.},
Title = {A Molecular Dynamics Study of the Effect of Ca{2+} Removal
on Calmodulin Structure},
Journal = {Biophys. J.},
Volume= {90},
Pages = {3842-3850},
Year = {2006}
}
@Article{Fyta2010,
author = Fyta, M and Kalcher, I and Dzubiella, J and Vrbka, L and Netz,
R R,
title = {Ionic force field optimization based on single-ion and ion-pair
solvation properties},
journal = J Chem Phys,
year = 2010,
volume = 132,
pages = 024911-024911
}
Ran.
sonali dhindwal wrote:
Hello All ,
I am also trying to simulate my protein with Mn ion present in it.
So can I create the topology entry for Mn ion similar to MG2+ ion ?
and how can I get the values of C6 and C12 leonard jones potential in
[atom type] entry and will it be required to add [nonbond_params] also
? how can I get them ?
Also I want to use Fe2+ also, but it is also not included in gromos
force field. This problem of adding other ions and molecule in the
system always remains. And being new to this field, can someone
suggest in simple terms how to include these considering the person is
not an expert in this field.
Please help.
--
Sonali Dhindwal
--- On *Tue, 8/6/10, Vitaly Chaban /vvcha...@gmail.com/* wrote:
From: Vitaly Chaban vvcha...@gmail.com
Subject: [gmx-users] Re: Simulation with CsCl
To: gmx-users@gromacs.org
Date: Tuesday, 8 June, 2010, 9:03 PM
Hi all:
I am trying to simulate a polysaccharide in solution of water
and CsCl, but
cesium is not parametrized in the gromacs 4. I am using the force
field GROMOS 96.
I have looked for the parameters of Cs+ in the OPLS Force field
and I have
created 4 files: Cs.atp, Cs.itp, Csnb.itp and Cs.rtp. Also I
have include
the parameters for Cs+ in the ions.itp file, but it didn't
work, Can
someone help me?
Thanks in advance.
Cecilia.
Cecilia -
You do not need so many files so cesium. Just copy your parameters to
the force field used and create the topology entry for cesium similar
to
[ moleculetype ]
Ar 1
[ atoms ]
1 Ar1Ar Ar0 0.0
Do not forget, cesium+ is an ion...
--
Dr. Vitaly Chaban
--
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--
--
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-639
Email: r.fried...@bioc.uzh.ch
Skype: ran.friedman
--
--
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Re: [gmx-users] How to increase the tolerance for conjugate gradient minimization
Hi Arthur, The most useful option from my experience is to run Gromacs in double precision. You also can try to make emstep smaller (after an initial minimisation of the crude structure) and use l-bfgs. Good luck, Ran -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- Arthur Roberts wrote: I agree the code is fine. Is there a parameter that I need to change to increase the tolerance? I have issues energy minimizing a small molecule in the presence of a macromolecule. One work around is to increase the energy of the small molecule, so that the macromolecule no longer dominates the energetics. I would appreciate your input. Art On Jun 4, 2010, at 5:45 PM, Mark Abraham wrote: - Original Message - From: Arthur Roberts aroberts99...@yahoo.com Date: Saturday, June 5, 2010 4:57 Subject: [gmx-users] How to increase the tolerance for conjugate gradient minimization To: gmx users gmx-users@gromacs.org Hi, all, Is there a way to increase the tolerance for Conjugate Gradient energy minimization? It seems that I can only get a Tolerance (Fmax) = 1e-4 emtol doesn't seem to do the trick. I tried several values. The code's fine in 4.0.7. Does your .mdp value match that reported in the .log file? Ditto in gmxcheck on the .tpr? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Art Roberts 7254 Shoreline Dr. #130 San Diego, CA 92122 cell: 206-850-7468 email: aroberts99...@yahoo.com skype=aroberts92122 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_cluster, RMSD distribution
Hi, The distribution is calculated as follows: 101 bins are formed between zero and maximum rmsd in equal separation (by calculating the largest value by 100 to create the separation). Each rmsd value is put into the right bin and the counter for that bin is increased by 1. The total number of counts is the size of half a matrix. Example: If the maximal rmsd is 10.0 and a certain comparison yield rmsd=0.13 the value of the second bin in increased by 1. Ran. Michał Koliński wrote: Dear All I’m trying to obtain RMSD distribution of a ligand in the binding site of the receptor protein during 40 ns MD simulation. Could you please explain: - what is exactly the yaxis unit of the plot obtained using g_cluster with –dist option - how is this distribution calculated? Thank you in advance, All best, Michal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] about SHAKE, SETTLE, LINCS and double x single precision
Hi Alan, I don't think using single precision is much of a problem when using thermostats, regardless of the constraint on the water. See also Berks' comments: http://oldwww.gromacs.org/pipermail/gmx-users/2010-March/049137.html http://oldwww.gromacs.org/pipermail/gmx-users/2010-March/049152.html Ran. Alan wrote: Hi there, From what I've read and known, here in the list as well, one of the main reasons why Gromacs run in single precision is because it has LINCS, besides SHAKE, which I believe requires double precision for accuracy. I am drawing such conclusion (that can be wrong) partially based on Lippert, R. A., Bowers, K. J., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., and Shaw, D. E. A common, avoidable source of error in molecular dynamics integrators. Journal of Chemical Physics 126, 4 (Jan. 2007), 046101–1–046101–2 However, in this letter article they didn't test with LINCS. I would love to hear some comments from Gromacs developers. When I started in MD, developing our own MD software, all was done in double precision, then came Gromacs blowing up this paradigm. (I am aware that even in Gromacs, there are routines that really requires double precision, e.g. normal mode analysis). Essentially I would like to understand better this double x single approach in MD re accuracy. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. http://www.bio.cam.ac.uk/~awd28 http://www.bio.cam.ac.uk/%7Eawd28 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein Aggregation using Gromacs
Hi, There's no recipie to locate aggregation hot spots based on MD simulations. There are many papers on simulations of protein and peptide aggregation from which you can draw some ideas, but bear in mind that aggregation of more than very few and very small peptides is typically much slower than what one can simulate using atomistic MD. For a quick approach you can use sequence analysis tools, e.g., TANGO http://tango.crg.es/ Good luck, Ran -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- shahid nayeem wrote: Dear all What are the analysis tools which should be used on MD trajectory file in order to find potential aggregation sites of a protein. Anyone can tell me about specific resource material on use of Gromacs to predict protein aggregation hot spots from MD trajectory anlysis. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein Aggregation using Gromacs
Hello again - IMHO the best approach for any simulation study is to plan how the simulation will be used to solve a specific scientific problem before running the simulations, rather then the other way around. To clarify what I wrote below, there's no algorithm I'm aware of where the input is an MD simulation of a certain protein and the output is an aggregation propensity of certain residues. Having said that, simulations can be a useful tool to study amyloid aggregation and even tendency of specific residues to aggregate first. A useful approach was developed in the group where I work now, based on the aggregation propensity of peptide sequences decomposed from the whole protein: http://dx.doi.org/10.1016/j.jmb.2006.01.009 Using your simulations, you can check if some residues are more prone to lose their secondary structure as the temperature increases, which suggests that they are more likely to unfold. Do bear in mind though that aggregation is a complex process which involves multimers. Unless you show some correlation with experimental findings it will be difficult to defend your conclusions. Ran shahid nayeem wrote: Hi I have used TANGO Aggrescan, Zyggregator and other online tools but I am unable to find and pinpoint residue responsible for aggregation. Then I did MD simulation of the proteins with gromacs at different temperature. Now in this background I need suggestion to analyse my MD trajectory. shahid Nayeem On 5/12/10, *Ran Friedman* r.fried...@bioc.uzh.ch mailto:r.fried...@bioc.uzh.ch wrote: Hi, There's no recipie to locate aggregation hot spots based on MD simulations. There are many papers on simulations of protein and peptide aggregation from which you can draw some ideas, but bear in mind that aggregation of more than very few and very small peptides is typically much slower than what one can simulate using atomistic MD. For a quick approach you can use sequence analysis tools, e.g., TANGO http://tango.crg.es/ Good luck, Ran -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch mailto:r.fried...@bioc.uzh.ch Skype: ran.friedman -- shahid nayeem wrote: Dear all What are the analysis tools which should be used on MD trajectory file in order to find potential aggregation sites of a protein. Anyone can tell me about specific resource material on use of Gromacs to predict protein aggregation hot spots from MD trajectory anlysis. Shahid Nayeem -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Normal Mode Analysis
Hi, NMA is not MD - for one thing you don't run an NMA simulation for a certain time. I suggest you read about NMA and make sure you understand what the method does and what it can achieve before continuing. There is some data on the manual, a lot of data on the web and even more in books. When you have a good idea on what is NMA and why you're interested in running it, you can try to run things and come back to the list with more specific questions if such arise. In parallel, it may be a good idea to read some papers where NMA was applied. I have in mind papers of Lindahl and Levitt from the recent years, but you should be able to come with an elaborate list. Good luck, Ran Anirban Ghosh wrote: Hi ALL, This may sound like a very basic question, but I am still pondering over it. I have simulated a membrane protein system for 30 ns after Steepest Descent minimization and now I want to perform NMA. From the help pages what I understand is that I need a very well minimized system (using l-bfgs) and then generate a Hessian matrix. My question is that after my 30 ns run, should I again go for another run of minimization with l-bfgs and the should I run MD using nm as the integrator? For how long should I run this MD with nm integrator? Is a 1 ns run enough? Or am I required to run it for 30 ns (for which I have run the normal MD)? Any suggestion is welcome. Thanks a lot in advance. Regards, Anirban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Dynamics cross correlation map
Hi Sukesh, I once put a version of g_covar that can calculate the correlations in the user contributions. Check if it's there or reply to me privately if you can't find it (though I'm on the road till Friday). Good luck, Ran On Wed, 24 Mar 2010 11:46:42 +0530 sukesh chandra gain suk...@atc.tcs.com wrote: Hi Tsjerk, Thank you for your reply. May be I was not very clear with my previous post. I am not looking for covariance / atomic covariances map (ie., covar.xpm/covara.xpm) which are generated by g_covar tool in GROMACS. I am particularly trying to get correlation map (example: http://www.pnas.org/content/102/4/994/F2.large.jpg, http://www.pnas.org/content/99/26/16597/F3.small.gif). I hope there is a difference between covariance matrix and correlation matrix. The correlated motions between two atoms is calculated as the magnitude of the co-relation coefficient between the atoms. In case of a system it can be assessed by examining the magnitude of all pairwise cross-correlation coefficients. The cross-correlation coefficient, C(i,j) for each pair of atoms i and j is calculated as: C(i,j) = delta r(i) * delta r(j) / sqrt sqr(delta r(i) ) . sqrt sqr(delta r(j) ) , where delta r(i) is the displacement from mean position of the ith atom and symbol represents the time average. This function returns a matrix of all atom-wise cross-correlations whose elements, C(i,j), may be displayed in a graphical representation frequently termed a dynamical cross-correlation map, or DCCM. If C(i,j) = 1 the fluctuations of atoms i and j are completely correlated, if C(i,j) = -1 the fluctuations of atoms i and j are completely anticorrelated and if C(i,j) = 0 the fluctuations of i and j are not correlated. Now my query is there any tool like g_correlation (http://www.mpibpc.mpg.de/home/grubmueller/projects/MethodAdvancements/GeneralizedCorrelations/index.html) by which I can get the cross-correlation matrix from covariance matrix or directly from trajectory file. Ref:1. Hünenberger PH, Mark AE, van Gunsteren WF; Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations; JMB 1995; 252:492-503 2. Oliver F. Lange, H. Grubmüller; Generalized Correlation for Biomolecular Dynamics; Proteins 2006; 62:1053-1061 Thank You, Regards, Sukesh -- Sukesh Chandra Gain TCS Innovation Labs Tata Consultancy Services Ltd. 'Deccan Park', Madhapur Hyderabad 500081 Phone: +91 40 6667 3572 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Skype: ran.friedman -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Turn-off water optimisation
Hi, Can you also post your .mdp? Ran Berk Hess wrote: Hi, I have never heard about problems like this before. It seems highly unlikely to me that the innerloops are causing this. Are your running exacly the same tpr file on your local machine and the cluster? You probably want to update to version 4.0.7 to be sure you have all the latest bugfixes. Please keep us updated on this issue, since things like this should never happen (unless there is a compiler bug). Berk Date: Fri, 5 Mar 2010 14:41:02 +0100 From: schl...@uni-mainz.de To: gmx-users@gromacs.org Subject: Re: [gmx-users] Turn-off water optimisation Hi, i have the following problem: (GROMACS 4.0.5) when i simulated water in serial on our cluster with the brendsen or v-rescale thermostat i get to high temperatures (300 K goes in very short time up to around 425 K). If i simulate in parallel or at my local machine i get no problems. Also if i change water to another molecule there are no such problems. (I use the same mdp file for all the simulations). Because the problem appears with water (spc and tip4p) but not with mesitylene i thought probably the special things for water (settle, and so on) could be the problem. So i wanted to simulate water without that fancy stuff. Thanks for the info with the enviroment variable, but where can i set it? For the other problems (why it works on the cluster in parallel, but not in serial, but works on the local-pc in serial) i have so far no idea, where to look. But first i'm happy to know if the problem comes from the special water-loops. Thomas Hi, You don't want to mess with the topology, you will be simulating a quit different system when you turn off constraints. Also Gromacs does not optimize based on names, since the name might not say anything about the molecule. I don't know what effect of what optimizations you want to test, but setting the environment variable GMX_NO_SOLV_OPT will turn off the special inner-loops for water. Berk Date: Fri, 5 Mar 2010 11:31:50 +0100 From: schlesi at uni-mainz.de To: gmx-users at gromacs.org Subject: [gmx-users] Turn-off water optimisation Dear all, I simulated water (spc) with the ffG53a5 force field. For testing propose i want to turn of the water optimisation. How do i do this? So far i have tried: * contraints = none * define = -DFLEXIBLE * took the spc.itp file and deleted all the stuff for settle and the other force fields, changed resname from SOL to WAT (also spc.itp - wat.itp) But all the time i the log file there is this line: Enabling SPC water optimization for 1184 molecules. Espically with the last option (change of the spc.itp) i don't how GROMACS recorgnises that i simulate SPC water, because i has a different name and so. Thanks for your help in advance. Greetings Thomas -- gmx-users mailing list gmx-users at gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php New Windows 7: Simplify what you do everyday. Find the right PC for you. http://windows.microsoft.com/shop -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] NVE of water
Hi Andrea, Did you use double precision? Also, I'd try a lower dt (say 1fs) and shake tolerance (maybe 1E-8). Good luck, Ran Andrea wrote: Dear users, for test purposes in order to set up a bigger system, I try to run NVE simulations of SPC water, but the energy increases very rapidely. My guess is that the cutoffs I use are not good for water. I that the case ( I would be grateful for a good reference for suitable SPC water parameters) or do I miss something else? My parameter file for the NVE is: title= NVE cpp = /lib/cpp integrator = md dt = 0.002 ; ps ! = 2 fs nsteps = 5 ; total 100 ps nstxout = 5000 nstvout = 5000 nstxtcout= 0 nstlog = 5000 nstenergy= 5000 nstlist = 10 ns_type = grid rlist= 1.1 unconstrained-start = yes constraints = all-bonds constraint_algorithm = shake shake_tol= 0.0001 ;VdW vdwtype = Switch rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist rvdw_switch = 0.9 gen_vel = no ; yes gen_temp = 300 gen_seed = -1 ;Temperature coupling tc_grps = system tcoupl = no ;nose-hoover tau_t= 0.1 ref_t= 300 ;Pressure coupling pcoupl = no optimize_fft = yes Any suggesions are really welcome. Thank you. Regards, Andrea Muntean -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] NVE of water
Hi, I would still argue that double precision is important. My comment on SHAKE was based on CHARMM - in Gromacs it indeed doesn't matter for water. Ran Justin A. Lemkul wrote: Berk Hess wrote: Hi, Shake is not relevant for water and also a time step of 2 fs should be fine. The cut-off's are the problem. You have a buffer size of 0.1 nm, which is already smaller than 2 times the distance from the center of geometry of a water molecule to a hydrogen. You need some additional distance for water diffusion. I would use a buffer of 0.25 to 0.3 nm. You don't list you coulombtype setting. Use pme (or if you want perfect energy conservation: pme-switch), you can also use reaction-field-zero if you really don't want to use PME. Then use nstlist=-1, run a short simulation and check in at the end of your log file that the neighbor list lifetime is somewhere between 5 and 20 steps. We should have a wiki entry for such details. Maybe there is one, but I was too lazy to check or make one. There was a basic NVE page; I have updated it based on your notes above: http://www.gromacs.org/Documentation/Terminology/NVE -Justin Berk Date: Mon, 1 Mar 2010 09:16:36 +0100 From: r.fried...@bioc.uzh.ch To: gmx-users@gromacs.org Subject: Re: [gmx-users] NVE of water Hi Andrea, Did you use double precision? Also, I'd try a lower dt (say 1fs) and shake tolerance (maybe 1E-8). Good luck, Ran Andrea wrote: Dear users, for test purposes in order to set up a bigger system, I try to run NVE simulations of SPC water, but the energy increases very rapidely. My guess is that the cutoffs I use are not good for water. I that the case ( I would be grateful for a good reference for suitable SPC water parameters) or do I miss something else? My parameter file for the NVE is: title = NVE cpp = /lib/cpp integrator = md dt = 0.002 ; ps ! = 2 fs nsteps = 5 ; total 100 ps nstxout = 5000 nstvout = 5000 nstxtcout = 0 nstlog = 5000 nstenergy = 5000 nstlist = 10 ns_type = grid rlist = 1.1 unconstrained-start = yes constraints = all-bonds constraint_algorithm = shake shake_tol = 0.0001 ;VdW vdwtype = Switch rvdw = 1.0 ; rvdw+ (0.1:0.3)= rlist rvdw_switch = 0.9 gen_vel = no ; yes gen_temp = 300 gen_seed = -1 ;Temperature coupling tc_grps = system tcoupl = no ;nose-hoover tau_t = 0.1 ref_t = 300 ;Pressure coupling pcoupl = no optimize_fft = yes Any suggesions are really welcome. Thank you. Regards, Andrea Muntean -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.uzh.ch Skype: ran.friedman -- -- 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/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php New Windows 7: Find the right PC for you. Learn more. http://windows.microsoft.com/shop -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] NVE of water
Berk Hess wrote: Date: Mon, 1 Mar 2010 15:44:28 +0100 From: r.fried...@bioc.uzh.ch To: gmx-users@gromacs.org Subject: Re: [gmx-users] NVE of water Mark Abraham wrote: On 2/03/2010 12:39 AM, Ran Friedman wrote: Hi, I would still argue that double precision is important. Oh? The discussion of Table 4 of http://pubs.acs.org/doi/abs/10.1021/ct700301q (2008 GROMACS 4 JCTC paper) suggested to me that single-precision NVE could be done well in GROMACS. Am I missing something? Mark The presented benchmarks were performed in the NVT ensemble (section IX). Or am I missing something? No, but everything that affects energy conservation in NVE also affects it in NVT, in addition the thermostat affect the integration accuracy in NVT (and in NVT you do not measure energy conservation from the total energy, but from the conserved energy quantity). Double precision can be important for energy conservation, but often other factors deteriorate the energy conservation orders of magnitude from what can be reached in single precision already. Double precision is only required for testing or when you really need to generate an NVE ensemble. Berk Thanks for clarifying Berk - I was referring to the latter (i.e., when you really need to generate an NVE ensemble). I guess this is the main reason to run with NVE. Since most people are not running NVE with large systems or for production simulations, the added accuracy often justifies the use of double precision. Best, Ran -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Assembling a good simulation starting point
Hello John, How large was the force after EM? Large forces often results in systems that explode during the simulation. Also, did you minimise with or without solvent? You assessment seems correct - the initial structure wasn't minimised and the tools of the trade are trying different conformations, minimising in vacuo at first and using other modelling tools before Gromacs. Also, read a bit in the mailing list and search the literature for similar studies. Good luck, Ran On Thu, 18 Feb 2010 19:08:11 -0800 (PST) John Ladasky blind.watchma...@yahoo.com wrote: Hello everyone, I'm a fairly new GROMACS user. I'm running GROMACS 4.0.5 on top of Ubuntu Linux 9.10. I am still learning a lot. I just tried to set up my first fairly complex simulation, and it failed. I have a protein of interest, a beta barrel with a hydrophobic, ligand-binding interior. I am interested in making mutations to this protein, with the goal of getting it to bind to a rather different ligand than the one it normally binds. The way that I propose to go about studying this problem is to construct a partially-unfolded version of the protein structure, add my ligand of interest, and then run an energy minimization. My first naive attempt to construct the partially-unfolded protein was not successful. I knew that it might have problems, but I tried it anyway. Using Biopython, I rotated the atomic coordinates so that the beta barrel was parallel to an axis. Then I simply pulled all of the atoms 3 Angstroms away from the axis. Finally, I inserted my ligand. Visually, inspecting the starting structure with PyMol, I didn't see anything egregious. However, I could have some unwanted close contacts. I got a few long bond warnings from pdb2gmx, but I persisted. I got through genbox, editconf, and my first grompp sucessfully. But then when I tried the first, position-restrained energy minimization, it aborted with too many LINCS warnings. I blew the system up. These LINCS warnings could come from close contacts, or from large forces in over-stretched bonds which resulted from my crude approach to expanding the protein structure. Whatever the cause, I need a smarter way to start. I am open to ANY suggestions! What I THINK I might want to do is to manipulate the starting structure in a more natural way. For example, selecting some peptide bonds in the beta turns, and changing their angles. A program which allows me to manipulate structures, and not just simulate natural forces, is what I think I need. Surely, people who have used GROMACS will have faced problems simliar to mine. Thanks for your advice! John Ladasky -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Skype: ran.friedman -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem normal mode analysis
Hi, I guess posting the whole set of commands you used and mdp file for NMA can help. Best, Ran sarbani chattopadhyay wrote: hi, I want to do a normal mode analysis on a small peptide. I had complied gromacs in double precision and energy minimized the structure in vacuum, using steepest descent followed by conjugate gradient method. the log file of conjugate gradient method reads Polak-Ribiere Conjugate Gradients converged to Fmax 0.0001 in 1023 steps Potential Energy = -1.95899271351756e+02 Maximum force = 9.50250289517625e-05 on atom 48 Norm of force = 3.82317661305055e-05 but when i try to run mdrun_d ( for normal mode analysis) , it shows Maximum force: 2.05241e+02 Maximum force probably not small enough to ensure that you are in an energy well. Be aware that negative eigenvalues may occur when the resulting matrix is diagonalized I had made grompp_d read the trajectory file of cg energy minimization by using the -t flag. where have i gone wrong? Any suggestion will be of great help. Thanks in advance. Sarbani Chattopadhyay http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline@middle? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problem with OPLS Benzene and Bond Constraints
Dear Mike, It's hard to know what's going on from your input. Did you check the thermodynamic components with g_energy (especially the pressure bond, LJ and Coulomb energies)? This may give you a hint. Also, I would do a test run with PME - you're anyway not following the parametrisation of Jorgensen and co-workers exactly. As a final note - the correct phase is something that's very difficult to reproduce exactly with classical MD, and while a single molecule interacting with a protein may work just fine, a bulk of such molecules does not always reproduce the correct phase at a given temperature. This is one reason why lipid models are still being developed. Hope that helps a bit, Ran Mike Wykes wrote: Dear All I would like to perform MD simulations with benzene as a solvent and am observing some strange behaviour when I use Lincs to constrain all the bonds. When I run a fully flexible NPT MD of a box of 320 benzene molecules simulation at 298K and 1bar, the density comes out at 841 g/l, not too far away from the experimental value of 876 g/l. However when I constrain all bonds using Lincs, the system expands rapidly, stabilising at a density of 2.62 g/l ! Both simulations started from NVT equilibrated simulations fixed to the experimental density. In the papers describing OPLS parametrisation, the MC simulations were indeed performed with fully flexible molecules, but it surprises me that the bond constraints would affect the density so strongly. Does anyone have any ideas why this is occurring? I am using a cutoff of 1.5 nm for VDW and Coulomb interactions without EWALD/PME but this is consistent with how OPLS was parametrised. There are no Lincs warnings in the log file of the constrained simulation. Please find my mdp and Benzene itp files below, the only difference between the flexible and constrained runs being dt = 0.001/0.002 and constraints = none/all-bonds respectively. Many thanks for your ideas/explanations as to what could be going on, Mike ; ; File 'mdout.mdp' was generated ; By user: mwykes (7017) ; On host: node168 ; At date: Thu Feb 4 20:05:46 2010 ; ; VARIOUS PREPROCESSING OPTIONS ; Preprocessor information: use cpp syntax. ; e.g.: -I/home/joe/doe -I/home/mary/hoe include = ; e.g.: -DI_Want_Cookies -DMe_Too define = -DFLEX_SPC ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit= 0 dt = 0.002 nsteps = 500 ; For exact run continuation or redoing part of a run ; Part index is updated automatically on checkpointing (keeps files separate) simulation_part = 1 init_step= 0 ; mode for center of mass motion removal comm-mode= LINEAR ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps= ; LANGEVIN DYNAMICS OPTIONS ; Friction coefficient (amu/ps) and random seed bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS ; Force tolerance and initial step-size emtol= 1.0 emstep = 0.1 ; Max number of iterations in relax_shells niter= 20 ; Step size (ps^2) for minimization of flexible constraints fcstep = 0 ; Frequency of steepest descents steps when doing CG nstcgsteep = 1000 nbfgscorr= 10 ; TEST PARTICLE INSERTION OPTIONS rtpi = 0.05 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file nstlog = 500 nstenergy= 500 ; Output frequency and precision for xtc file nstxtcout= 500 xtc-precision= 1000 ; This selects the subset of atoms for the xtc file. You can ; select multiple groups. By default all atoms will be written. xtc-grps = BNZ ; Selection of energy groups energygrps = BNZ ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) nstype = grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist= 1.5 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 1.5 ; Relative dielectric constant for the medium and the reaction field epsilon_r= 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths
Re: [gmx-users] intrapeptide hbond existence map
Hi Stephane, The map shows weather a certain hydrogen bond exists at a certain time. In principle you can get the information by integrating this data, but I'm not sure it can be done without changing the code. A possible solution is to use a script and run g_hbond -num 28 times with two relevant groups (N-H donor and oxygen acceptor), and calculate the occupancy based on this (I guess you mean the fraction of time that this h_bond existed. Ran. ABEL Stephane 175950 wrote: Hi everybody, I am doing some analysis of the interpeptidique hbonds (INTRHB) during the aggregation in beta fuof 4 heptapeptides in water I have defined in a index file the Acceptor-Donor-Hydrogen atoms list for the 28 INTRHB like this NH--CO [intra_hbds] 4 17 5 18 26 19 27 43 28 44 52 45 53 60 54 to obtain the INTRHB existence map i used the command with gmx4.05 g_hbond_mpi -n 4_Peptide_53A6_hbonds.ndx -s 4_Peptide_53A6.tpr -f ./XTC/Whole_Traj_53A6Center.xtc -b 40 -e 50 -hbn 4_Peptide_53A6_hbonds_400_500ns_index -hbm 4_Peptide_53A6_hbonds_400_500ns_Map The map show in the x and y axis the time and residue (up to 84). I have no idea what the figure means. The olot is stored here http://www.st-abel.com/Hbond_occupency.jpg I want only to know if, for example, the Hbond_occupency for the group NH or CO of the residu 1 Thank you in advance for your help Stephane -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] ice.pdbice.itp
fairuz zulkifli wrote: Hello everybody, I'm Fairuz from Malaysia. I just want to ask if there is someone that have information about PDB of ice and itp file of ice. I only had PDB of the ice and trying to convert it into itp file using GAMESS software. You can't. A .pdb file is a coordinate file, while an .itp is a parameter file (topology). The two are not interchangeable. I presume that you can use the parameters for water and simulate at a suitable temperature, though. -Justin Not always - that depends on what you want to study. It's very difficult to get realistic presentations of ice in MD, and the freezing temperature of water models is usually not 273K. There are some works on the subject, using an initial model prepared according to geometric specifications. I remember something from Victoria Buch but there may be newer studies around. Ran. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Locally Enhanced Sampling with Gromacs
Hi, LES as developed by Elber is available in CHARMM and MOIL. Ran. Massimiliano Bonomi wrote: Hi! You may want to try PLUMED, which is the evolution of grometa http://merlino.mi.infn.it/~plumed/PLUMED/Home.html and can do also steered MD and umbrella sampling. Massimiliano On Jan 27, 2010, at 8:48 AM, David van der Spoel wrote: On 1/27/10 7:49 AM, swa...@ncbs.res.in wrote: Dear Dr. Spoel, I am garduate student in National Centre for Biological Sciences(NCBS-TIFR), India. I am willing to do Locally Enhanced Sampling(LES) in one my research project.I saw few webpages on LES using GROMACS but not able to find any proper documentation/tutorial on that. Would you please help me regarding the same?? Thanks, Regards, Please keep questions on the list. Gromacs implements Flooding and Replica Exchange, both are well documented. In addition you can use metadynamics (similar to flooding) with gromacs if you install grometa. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Problems with g_hbond
Hi Rolf, Try renaming the atom names to something that starts with O and H for oxygen and hydrogen. Good luck, Ran. Rolf Erwin Isele-Holder wrote: Dear users, I'm running a simulation which uses ethanol as solvent. When using g_hbond the programm is able to recognize the solute's donors and acceptors, however it does not recognize any acceptors or donors of ethanol. Here is a part of my topology: [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 HO 1 ETHH EH 1 0.398 1.008 ; qtot 0.398 2 OA 1 ETHH EO 1 -0.54815.9994 ; qtot -0.15 3CH2 1 ETHHEC1 1 0.15 14.027 ; qtot 0 4CH3 1 ETHHEC2 2 0 15.035 ; qtot 0 [ bonds ] ; aiaj functc0c1c2c3 1 2 1 2 3 1 3 4 1 Why doesn't g_hbond recognize any donors or acceptors? Regards, Rolf -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_mindist -or inconsistencies with atom-pairs
Dear Shay, What do you get when -or is present? Do the atoms always belong to the same residues? I suspect that since the calculation of the minimal distance is made for all residues, what you get at the end is the atoms at minimal distance between the last two residues. This seems like a bug and I suggest you submit a bugzilla. As a side note I think that the output will be given only for the last two groups in case there are more than two. You may want to check this as well if you submit a bug report. It should be too difficult to fix, but would involve changes in a few places in the code. Best regards, Ran. shaya...@post.tau.ac.il wrote: Dear Gromacs users, We used g_mindist analysis as follows: g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg -or res_mindist.xvg and surprisingly in the atom-pairs.out only several atoms in one residue (from group 1) were at minimum distance from group 2 throughout the entire simulation. Checking this output manually showed it to be incorrect. res_mindist.xvg seems to hold the correct data. When running the same analysis, only omitting the -or flag, we get a *correct* atom-pairs.out. g_mindist -f *.xtc -s *.tpr -o atom-pairs.out -od mindist.xvg Comparing mindist.xvg from both scenarios shows no difference (files are identical). Is the -or flag supposed to affect the other output files of the g_mindist function? Supplementary details: 1. The same thing happened when g_mindist -s was supplied with either .gro, .pdb or .tpr files. 2. Index-groups 1 and 2 consisted upon full molecules with no ommisions (full protein and not only C-alpha). 3. We ruled out PBC by using -nopi 4. This is common with the following Gromacs versions: 3.3.3., 4.0.5, 4.0.7. Regards, -Shay --gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] reference for make_edi -linacc
Hi Chris, Maybe in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1303567/ Daidone et al., Molecular Dynamics Simulation of Protein Folding by Essential Dynamics Sampling: Folding Landscape of Horse Heart Cytochrome c Ran. chris.ne...@utoronto.ca wrote: Hello, does anybody have a reference for the -linacc method applied by make_edi/mdrun? I have checked the references mentioned in make_edi -h as well as the manual, but didn't find anything that matches -linacc exactly. For example, gromacs suggests that entire MD steps will be accepted or rejected if they do or do not move in the desired direction along the selected eigenvectors, respectively: -linacc: perform acceptance linear expansion along selected eigenvectors. (steps in the desired directions will be accepted, others will be rejected). While the published version appears to be more complex: B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; An extended sampling of the configurational space of HPr from E. coli PROTEINS: Struct. Funct. Gen. 26: 314-322 (1996) Briefly, the algorithm consists of the following steps: a starting position is defined as the set of essential coordinates of the starting conformation; a number of regular MD steps is preformed; for each step, a new starting position is accepted only if it is not closer to the starting position than the previous position, in the subspace defined by the first three eigenvectors (i.e., if the distance from the starting position in this subspace does not decrease). If the new position is closet to the starting position, a correctio is applied only in the subspace defied by the first three eigenvectors with least perturbation. Thank you, Chris. --gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] using trjconv to get a 2x2x2 unit cell for traj.xtc
Dear Jenny, You can do this directly in VMD, using the Periodic tab under Graphics-Representations. Ran Jennifer Williams wrote: Hello, I am trying to find a way around a visualisation problem I am having in VMD. Some of my molecules go over periodic boundary conditions meaning that bonds sometimes appear missing when looking at movies (I am trying to fix this using wrap, unwrap and join in VMD but as yet no luck). I was wondering if there is a way in gromacs to multiply the number of unit cells shown in a trajectory. i.e instead of a 1x1x1 I want the new unit cell to be 2x2x2. This would mean the section of the structure I want to zoom in doesn't go over the pbc. For the confout.gro file I have done this using genconf -nbox 2 2 2 -f confout.gro -o confbig.out and this enables me to at least see a static image where all bonds are present. but in order to view a movie, I need to carry out something similar on the traj.xtc file. I have seen that with trjconv there is the option -box Size for new cubic box but my unit cell is not cubic, it is a parallelepiped. The cell dimensions are : 4.64210 3.77847 1.89596 0.0 0.0 -2.18150 0.0 0.0 0.0 I tried using this anyway with the following command: trjconv -box 9.28414 8.72598 3.79192 -f traj.xtc -o trajbig.xtc but the resulting .xtc file wouldn't load into VMD so I assume that the .xtc file and the .gro file didn't match. Any ideas?, Thanks Jenny --The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. --gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Docking with PyMol and using Gromacs
With VMD it's even simpler: use dynamic bonds. Ran. Nicolas Sapay wrote: Dallas B. Warren a écrit : Coordinate files like pdb and gro aren’t used by GROMACS to provide any bonding information. That is what the topology files are for. So their “presence” in your pdb isn’t an issue. Actually, what is probably happening is that PyMol is guessing the bonds presence, based on the distance between atoms, and displaying it (which is what VMD does as well). So the bonds aren’t actually there at all in the pdb file. VMD can read/write CHARMM/NAMD topology files (namely psf files). If your problem is *just* a visualization artefact, you can load your structure in VMD, write a psf file and delete the unwanted bonds (this does not require a specific forcefield). You can also combine 2 psf files (1 for your protein and 1 for your ligand), that require some basic knowledge of TCL though. After that, you just have to load the topology abd the coordinates: vmd -psf topology.psf -pdb coordinate.pdb You won't see any weird bonds. Nicolas Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - When the only tool you own is a hammer, every problem begins to resemble a nail. *From:* gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Gunnar Widtfeldt Reginsson *Sent:* Thursday, 12 November 2009 10:13 AM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Docking with PyMol and using Gromacs Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open the DNA file in pymol and then load the organic molecule. After docking the organic molecule I write save name.pdb When viewing the name.pdb file in pymol there are some bonds between the organic molecule and the DNA that I don't want. Somehow pymol creates them and I don't see those bonds in the name.pdb file when I open it in a text reader. I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro files and convert into a .pdb with editconf The newly created pdb file still has those unwanted bonds. My question is: Can I ignore those bonds? If not, how can I prevent pymol making those bonds? Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Constraints Restraints
Erik Marklund wrote: Mark Abraham skrev: Darrell Koskinen wrote: Hi Tsjerk, So then, if I understand correctly, setting constraints = all-bonds is not as realistic as setting constraints = none, since the latter will allow for flexible (e.g. harmonic) behavoir which is more realistic than fixing the bond to a certain distance, correct? Actually not. It would be a better model of a harmonic potential (duh), but it has been shown that the use of constraints can lead to a (more?) acceptable model of a real system, and they allow a larger integration time to boot. Check out the papers for the constraint algorithms (refs in GROMACS manual). Mark Agreed. And this is especially true for hydrogen atoms as I understand it, since their behaviour as quantum particles deviate more from a classical treatment than is the case for heavier nuclei. This is mentioned in the gromacs manual. /Erik This depends on the system you study. In some cases it is necessary not to constrain the hydrogen atoms to get a better agreement with the experiment. Also, if one needs to deal with vibrational spectra involving hydrogens, they must be mobile. Ran. Date: Wed, 11 Nov 2009 21:45:44 +0100 From: Tsjerk Wassenaar tsje...@gmail.com Subject: Re: [gmx-users] Constraints Restraints To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 8ff89815091245u63c6aa65sa839f24634352...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 Hi Darrell, Constraints and restraints also apply to relative positions. A bond constraint fixes the bond to a certain distance. constraints = all-bonds means that all bonds are to be converted to constraints, rather than have them flexible, e.g. harmonic. Harmonic bonds are actually more like restraints, penalizing deviations from the equilibrium values. These equilibrium values and the 'penalty function' are described in the force field. Hope it helps, Tsjerk On Wed, Nov 11, 2009 at 9:32 PM, darre...@ece.ubc.ca wrote: Hi, I just have a quick question on contraints and restraints. My understanding is that constraints fix the position of an atom in space and restraints restrain the deviation of the atom's position from its equilibrium point. Is that correct? If so, then I am a little confused by the purpose of constraints = all-bonds or constraints = none in an mdp file, since by selection of a force field, which has bond/angle/dihedral stretching/bending/torsion constants, we are specifying the constraints applied to the simulation. So then what is the purpose of constraints = all-bonds and constraints = none? Thanks. Darrell -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Hydrogen bond occupancy for the dimer of Acetic Acid
Hi Rasmus, A simple solution would be to run g_hbond twice, with two separate groups for acetate 1 as donor and acetate 2 as acceptor or vice versa, check the existence an hydrogen bond with g_hbond -num and write a script to check when the two hydrogen bonds co-exist. Hope that helps, Ran. Rasmus Termo Lundsgaard wrote: Hi All. I'm trying to calculate the Hydrogen bond occupancy when there is two hydrogen bonds between same two acetic acid molecules at the same time. With g_hbond I can get the hbond.ndx giving me all ocuring hydrogen bonds group and the hbmap.xpm gives me the matrix of when these hydrogen bonds exist for each timeframe... How can I calculate the occupancy of when two hydrogen bonds exist between the same two molecules?? Best regards Rasmus -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Hydrogen bond occupancy for the dimer of Acetic Acid
Hi Rasmus, From your previous email I understood that you have only two molecules (you didn't write that you're using 500 and nothing on the rest of the system). Apparently, this is not the case. I don't think you can get what you want from g_hbond without modifying the source code. If you don't mind 500 runs you can use g_dist -dist, where group 1 is a single hydrogen bond donor oxygen and group two all potential acceptors, find the molecules which satisfy your criterion and then run g_hbond on them if you want to be sure that you have a hydrogen bond that satisfy angle criteria as well. Tedious, but can work with some scripting and patience. Ran. Rasmus Termo Lundsgaard wrote: Hi Ran. If I understand you right, then you suggest to have one molecule as acceptor, and the rest (499) as donors, and then look in the hbnum.xvg to see how often there is two hydrogen bonds... 1. is that I have to do this check for every molecule. 2. there is no guaranty that the two hydrogen bonds are to the same other molecule - it could very well be as a part of a chain... 3. If possible I would like to do measurement of distance between molecules when they are bonded as a dimer... Best regards Rasmus Ran Friedman wrote: Hi Rasmus, A simple solution would be to run g_hbond twice, with two separate groups for acetate 1 as donor and acetate 2 as acceptor or vice versa, check the existence an hydrogen bond with g_hbond -num and write a script to check when the two hydrogen bonds co-exist. Hope that helps, Ran. Rasmus Termo Lundsgaard wrote: Hi All. I'm trying to calculate the Hydrogen bond occupancy when there is two hydrogen bonds between same two acetic acid molecules at the same time. With g_hbond I can get the hbond.ndx giving me all ocuring hydrogen bonds group and the hbmap.xpm gives me the matrix of when these hydrogen bonds exist for each timeframe... How can I calculate the occupancy of when two hydrogen bonds exist between the same two molecules?? Best regards Rasmus -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center
For quite a long time I had the feeling that trjconv doesn't resolve all situations. Following the very recent discussion between Roland Schutz and Tsjerk, I'm not sure there is an immediate solution. Ad hoc approaches such as preparation of tpr files from intermediate snapshots were useful for me in some cases, so you can try these. For calculations of distances you can sometimes calculate the shift and apply an a posteriori fix, but that won't work for visualisation and isn't a robust solution. I don't think it has anything to do with the MARTINI FF. Ran. maria goranovic wrote: So lets say that I delete the first frame from the trajectory in which some atoms might have been outside the box. Everything should be within the box once the simulation starts (from the second frame onwards)? So the procedure should work if the reference structure is the second frame? I have tried that, and it fails as well. On Thu, Nov 5, 2009 at 4:40 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: The nojump option will not apply the pbc when an atom is crossing the box boundaries ... in your case your bilayer should definitely be in the center of your box and all the atoms in If not ot course it does not work! On Nov 5, 2009, at 4:33 PM, maria goranovic wrote: my starting structure looks quite all right to me. everything is in the box (except the tails of some lipids) .. wonder whats wrong. thank you verymuch for helping On Thu, Nov 5, 2009 at 4:04 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: On Nov 5, 2009, at 4:00 PM, maria goranovic wrote: Hi Xavier, Thanks for the clear instructions. The bilayer is not in one piece in the z direction after the -pbc nojump for some reason. the problem might be from your starting structure, everything should be in the box! Or you may be facing strange/funny/incomprehensible behavior ... after the third step, the water is in the right place, but the bilayer has expanded to periodic boxes in the xy plane. so the center of mass of the lipid molecules is not really being centered in the box ? On Thu, Nov 5, 2009 at 3:34 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: you need to do: 1- trjconv -pbc nojump; this keeps your bilayer in one piece on the z direction 2- trjconv -center; using the bilayer to center and the system as output; this will translate your bilayer on the z axis and normally not modify it on the xy plan. 3- trjconv -pbc mol; will put your lipids in one piece in the box; I believe this step cn be coupled to the previous quite safely. On Nov 5, 2009, at 3:23 PM, maria goranovic wrote: One more note about -pbc nojump. I typically use -pbc mol. Using pbc nojump succeeds in keeping the center of the bilayer at 0 0 0, but the atoms have moved way out of the simulation box resulting in a dilute system On Thu, Nov 5, 2009 at 2:31 PM, maria goranovic mariagorano...@gmail.com mailto:mariagorano...@gmail.com wrote: Centering on one atom has a problem that the lipid diffuses in the plane of the membrane, and as a result, the entire system starts to center around the lipid resulting in a simulation box which translates a lot in the bilayer plane. The splitting is not a problem, yes. But during the simulation period when the bilayer is not split, it diffuses quite a bit along the bilayer normal (after use of -pbc mol, and centering around the lipid center of mass). a plot of the lipid center of mass shows the bilayer diffusing along z, when its not split. On Thu, Nov 5, 2009 at 2:25 PM, XAvier Periole x.peri...@rug.nl mailto:x.peri...@rug.nl wrote: On Nov 5, 2009, at 2:02 PM, Justin A. Lemkul wrote: maria goranovic wrote: I did use -pbc nojump, but that does not help What about entering on a central lipid tail atom, I suggested some time ago? The bilayer probably just splits across periodic boundaries, so this is not really a problem; just a visualization artefact. The splitting is not a problem and I think that centering using one lipid (tail) won't change
Re: [gmx-users] Is anyone also using lammps?s
Dear Peng, Did you also try to run GMX in double precision at some point? Ran Peng Yi wrote: I turned off the torsion interaction. The difference between Lammps and Gromacs at integration time step 2fs was reduced. Details below: A melt of 240 n-octane (united-atom model), NVT, T=300K, V=55.46nm^3. Both Lammps and Gromacs use berendsen thermostat with tau_t=1ps. Integration time step 1fs: LammpsGromacsStd. Err. (for both) Ebond(kJ/mol):2092 2109 100 Eangle: 1778 175480 Elj+corr: -10501-10553 100 T(K): 300 299 5 P(atm): 3188 3016 700 integration time step 2fs: LammpsGromacsStd.Err. (for both) Ebond:2133 2232 100 Eangle: 1803 173780 Elj+corr: -10501-10623 100 T: 300 298 5 P:3133 2955 600 Lammps results remain almost unchanged when dt increases from 1fs to 2fs, and Ebond : Eangle = 7 : 6, which is the ratio between # of bonds and # of angles. Gromacs results change more significantly when dt goes from 1fs to 2fs. and the trend of Ebond and Eangle are opposite. It is more significant when torsion interaction is present. On Tue, 3 Nov 2009, David van der Spoel wrote: Peng Yi wrote: Hi, David, I used Berendsen thermostat and a bigger tau_t=1ps to redo the simulations. The general conclusion is the same. The std err is the same in both packages. And during each simulation, the integration time does not change. Details below: Integration time step 1fs: Lammps GromacsStd.Err. (for both) Ebond(kJ/mol): 21122170 100 Eangle: 17991770 100 Etors: 25522490 100 Elj+corr: -10711 -10777 100 P(atm): 32503216 500 Integration time step 2fs: Lammps GromacsStd.Err. (for both) Ebond: 21542654 120 Eangle: 18401645 120 Etors: 25732236 120 Elj+corr: -10711 -11019 100 P(atm): 3250 2590 600 How about the temperature in both systems? Was Lammps also run with Berendsen? It could also still be a topology error. Maybe you can turn off the torsion potential to test this. -Peng On Sun, 1 Nov 2009, David van der Spoel wrote: Peng Yi wrote: Thank for your reply! I have done some NVT runs per your suggestion, and the results are similar to NPT runs, i.e., Gromacs results is more affected by changing integration timestep than Lammps. Details below: A melt of 240 octane chains by united-atom model. T=300K, V=55.46 nm^3. Both Gromacs and Lammps use Nose-Hoover thermostat with tau_t=0.2 ps. As some people have note the tau_t is short for Nose Hoover. Are you sure this means the same in Lammps and in Gromacs? For one thing, there is no tau_t in the NH algorithm as far as I know, and Gromacs converts it to an appropriate weight or whatever that is called. What does Lammps do with this tau_t. To be a the safe side you could run both with Berendsen as well. Is the std err identical in both packages? And in the 2 fs run, are both simulation equlibrated with this time step as well? All other parameters in .top and .mdp files are the same as previously attached.. If I use integration time 1fs, Lammps and Gromacs produce consistent results: Lammps Gromacs std. err. Ebond(kJ/mol):21332160 100 Eangle: 17571780 80 Etors:25312510 80 Elj+corr: -10711 -10767 90 P(atm): 35003250 500 if I use integration time 2fs, Lammps results remain unchanged, but Gromacs results change significantly, particularly bonded energy: Lammps Gromacs std. err. Ebond(kJ/mol):21752710 100 Eangle: 17991640 70 Etors:25732230 80 Elj+corr: -10711 -11007 100 P(atm): 3200 2730 700 Would that be a result of using different integrator between Lammps and Gromacs? Lammps uses Velocity-Verlet, and Gromacs uses Leap-frog. Thanks, -Peng On Thu, 29 Oct 2009, David van der Spoel wrote: aherz wrote: Hey, are you running single or double precision gromacs? Afaik, depending on the circumstances the energy drift in gromacs can be rather bad for single precision. Please refer to the gromacs 4.0 paper for a discussion of the drift. If you want to compare energies you need the same density, which you do not have, you may need to run NVT for
Re: [gmx-users] Is anyone also using lammps?s
Hi Peng, AFAIK GMX only uses fftw for PME. If you have no reason to prefer flexible bonds you can use LINCS or SHAKE to constrain the bond lengths and run with a timestep of 2fs at room temperature. You may want to try LAMMPS and GMX with SHAKE and a timestep of 2fs and see if the results are similar before recompiling GMX. If I understood you correctly you didn't constrain the bonds. Ran Peng Yi wrote: Hi, Ran, Do you mean the simulation I used here for testing purpose? That is not long, maybe a few hours. But my research will require simulations for days. If I will not use PME, do I still need a fftw? -Peng On Wed, 4 Nov 2009, Ran Friedman wrote: Hi Peng, It would be slower - never made any benchmarks on how much slower. But you don't run a very long simulation, do you? Installing it isn't a problem. If you use PME you also need fftw in double precision though. Ran Peng Yi wrote: Hi, Ran, No, I haven't. I still have to find out how to install in double precision. Would double precision be slower than single? If so, how much? Or just double the memory used? Thanks, -Peng ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] % of existence of hydrogen bond
Hi, You can use g_hbond -num and write a small script to calculate the percentage of h-bond existence per frame by calculating the number of frames for which a h-bond exists. Good luck, Ran. Moutusi Manna wrote: Dear all, I am dealing with a POPC+PEPTDE+WATER system. Basic residues of the peptide make hydrogen bonds with lipid headgroup (as reflected from g_rdf analysis) and the number of hydrogen bonds formed can be calculated from g_hbond program. Now, i want to calculate the % of trajectory time for which a bond between a particular group (say LYS and lipid headgroup po4) exist. -hbm gives a .xpm matrix, on solving (using xpm2ps) that i got a .eps file, which is a picture file of h_bond existence map, but the data sheet is not given. Can any one help me to solve this problem? With regards, Moutusi Manna Add whatever you love to the Yahoo! India homepage. Try now! http://in.rd.yahoo.com/tagline_metro_3/*http://in.yahoo.com/trynew ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Is anyone also using lammps?s
Hi Peng, Note that you're not using any bond constraints in Gromacs and a timestep of 2fs may be too long. Also, tau_t=0.02 seems too short for me. With 1fs timescale the agreement seem good enough, but you didn't include estimated errors so it's hard to tell. Also, I assume you run GMX in single and LAMMPS in double precision. Did you check for convergence? Ran Peng Yi wrote: On Wed, 28 Oct 2009, Mark Abraham wrote: Peng Yi wrote: I am trying to simulate alkane melt and found out that gromacs and lammps gave different results, particularly the bonded interaction energy. I wonder if anyone has such experience. Thanks, Even two installations of the same version of GROMACS can give different results. The question is whether when using comparable model physics you observe the same ensemble averages. Mark Hi, Mark, Thanks for reply! The difference is statistically significant. And I am wondering if it is caused by the integrator: Leap-frog for Gromacs and Velocity-verlet for Lammps. Detail description of the comparison please see below: It is an NPT simulation of a melt of 240 n-octane molecules using united-atom model, i.e., CHx group is considered as one atom. There are bond, angle, torsion and LJ interactions. T=300K and P=1atm. Lammps uses nose-hoover thermostat and barostat, and Gromacs uses nose-hoover thermostat and Parranello-Rahman barostat. Time constants for thermostat and barostat are 0.02ps and 2.0ps, respectively. If I use integration time 1fs, Lammps and Gromacs gave consistent results: Lammps Gromacs Ebond(kJ/mol):2092 2146 Eangle: 1757 1760 Etors:2510 2500 Elj+corr:-9238-9350 Volume(nm^3): 66.7 66.5 where energy fluctuation is 100 kJ/mol and volume fluctuation is 1 nm^3, Elj+corr is the total LJ energy including tail correction. However, if I use integration time 2fs, Lammps results do not change much, but Gromacs results changed a lot: Lammps Gromacs Ebond(kJ/mol):2133 2700 Eangle: 1799 1640 Etors:2552 2200 Elj+corr:-9292-9886 Volume: 66.7 64.0 The results given by Lammps is more reasonable because the Ebond should be equal to the total # of bonds times 1/2k_BT and Eangle should be equal to the total # of angles times 1/2k_BT. At T=300K, 1/2k_BT=1.25 kJ/mol. 240 n-octanes have total 1680 bonds and 1440 angles. The bond and angle interactions are both harmonic functions. Bond interaction constant kl=292880 kJ/mol/nm^2, corresponding to a bond ossilation period 16 fs. Is there something related to the integrator? Here I attached my grompp.mdp and topol.top files. ## grompp.mdp ## ; VARIOUS PREPROCESSING OPTIONS title= Yo cpp = /usr/bin/cpp include = define = ; RUN CONTROL PARAMETERS integrator = md tinit= 0 dt = 0.001 nsteps = 200 init_step= 0 comm-mode= Linear nstcomm = 1 comm-grps= ; OUTPUT CONTROL OPTIONS nstxout = 5000 nstvout = 5000 nstfout = 5000 nstcheckpoint= 1 nstlog = 1000 nstenergy= 1000 nstxtcout= 5000 xtc-precision= 1000 xtc-grps = energygrps = ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ns_type = grid pbc = xyz rlist= 1.0025 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 1.0025 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0; default rvdw = 1.0025; default 1 nm DispCorr = EnerPres ;table-extension = 1.5 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS Tcoupl = nose-hoover tc-grps = System tau_t= 0.02 ref_t= 300.0 Pcoupl = Parrinello-Rahman Pcoupltype = isotropic tau_p= 2.0 compressibility = 4.5e-5 ref_p= 1.0 andersen_seed= 815131 ; GENERATE
Re: [gmx-users] Is anyone also using lammps?s
Hi Peng,
The time scale should be much shorter than the fastest vibration. A rule
of thumb from the reference below is a factor of ten, but it would
depend on the precision. Running with double precision is shorter but I
didn't make benchmarks (perhaps other users have).
Appropriate values of tau_t and tau_p have also been discussed in this
list (search for references by Berk). I tend to use something like
tau_t=0.2 and tau_p=1.0.
I advise you to follow David's suggestion as well and run with NVT.
Ran.
Reference:
@book{Becker2001,
Author = {Becker, O. M. and MacKerell, A. D. Jr. and Roux, B. and
Watanabe, M.},
Title = {Computational biochemistry and biophysics},
Publisher = {Dekker, M.},
Address = {New York},
Year = {2001} }
Peng Yi wrote:
Hi, Ran,
I didn't use bond restraints. I checked that the bond length had a
Gaussian-like distributes, and the length range looked normal.
I estimated the fastest timescale in the system, which is the bond
ossilation period, around 16fs. Would that require as integration
timestep much smaller than 1fs?
With the parameters I have, could you recommend a set of tau_t and tau_p?
I did mention the fluctuation, 100 kJ/mol for energy and 1 nm^3 for
volume. And I ran GMX in single. Not sure about Lammps, should be
double. All measured physical quantities converged well. Would you
expect differece if I compile GMX in double? Would that be much slower?
-Peng
On Thu, 29 Oct 2009, Ran Friedman wrote:
Hi Peng,
Note that you're not using any bond constraints in Gromacs and a
timestep of 2fs may be too long.
Also, tau_t=0.02 seems too short for me.
With 1fs timescale the agreement seem good enough, but you didn't
include estimated errors so it's hard to tell. Also, I assume you run
GMX in single and LAMMPS in double precision. Did you check for
convergence?
Ran
Peng Yi wrote:
On Wed, 28 Oct 2009, Mark Abraham wrote:
Peng Yi wrote:
I am trying to simulate alkane melt and found out that gromacs and
lammps gave different results, particularly the bonded interaction
energy.
I wonder if anyone has such experience. Thanks,
Even two installations of the same version of GROMACS can give
different results. The question is whether when using comparable
model physics you observe the same ensemble averages.
Mark
Hi, Mark,
Thanks for reply! The difference is statistically significant. And
I am
wondering if it is caused by the integrator: Leap-frog for Gromacs and
Velocity-verlet for Lammps. Detail description of the comparison
please
see below:
It is an NPT simulation of a melt of 240 n-octane molecules using
united-atom model, i.e., CHx group is considered as one atom. There
are
bond, angle, torsion and LJ interactions. T=300K and P=1atm.
Lammps uses nose-hoover thermostat and barostat, and Gromacs uses
nose-hoover thermostat and Parranello-Rahman barostat. Time constants
for
thermostat and barostat are 0.02ps and 2.0ps, respectively.
If I use integration time 1fs, Lammps and Gromacs gave consistent
results:
Lammps Gromacs
Ebond(kJ/mol):2092 2146
Eangle: 1757 1760
Etors:2510 2500
Elj+corr:-9238-9350
Volume(nm^3): 66.7 66.5
where energy fluctuation is 100 kJ/mol and volume fluctuation is 1
nm^3,
Elj+corr is the total LJ energy including tail correction.
However, if I use integration time 2fs, Lammps results do not change
much, but Gromacs results changed a lot:
Lammps Gromacs
Ebond(kJ/mol):2133 2700 Eangle:
1799 1640
Etors:2552 2200
Elj+corr:-9292-9886 Volume:
66.7 64.0
The results given by Lammps is more reasonable because the Ebond should
be equal to the total # of bonds times 1/2k_BT and Eangle should be
equal
to the total # of angles times 1/2k_BT. At T=300K, 1/2k_BT=1.25
kJ/mol.
240 n-octanes have total 1680 bonds and 1440 angles.
The bond and angle interactions are both harmonic functions. Bond
interaction constant kl=292880 kJ/mol/nm^2, corresponding to a bond
ossilation period 16 fs.
Is there something related to the integrator?
Here I attached my grompp.mdp and topol.top files.
##
grompp.mdp
##
; VARIOUS PREPROCESSING OPTIONS
title= Yo
cpp = /usr/bin/cpp
include = define =
; RUN CONTROL PARAMETERS
integrator = md
tinit= 0
dt = 0.001
nsteps = 200
init_step= 0
comm-mode= Linear
nstcomm = 1
comm-grps=
; OUTPUT CONTROL OPTIONS
nstxout = 5000
nstvout = 5000
nstfout = 5000
Re: [gmx-users] g_hbond and fluor
David van der Spoel wrote: Alvaro Cortes wrote: Hi all. I'm new at the list so i don't know if something similar has been discussed before. I tried to search in the archives, but i can't find something similar. I have a doubt about g_hbond and fluor acceptors. As i can see in the code, no parsing of F atoms is done in search_acceptors function in gmx_hbond.c, so i added || ((*top-atoms.atomname[n])[0] == 'F') || between oxygen and nitrogen parsing. This results in an increase of the number of hbonds reported by the program but i dont know if this little change is enough or even correct. Someone can bring me light in this stuff? I think it should be correct. Obviously it would be good to be more flexible without the need for user programming. In some contexts one might want to look for C-H ... 0 bonds as well and even N-H ... Aromatic interactions. A bit off topic from the fluor-related issue, but if you modify g_hbond, maybe it makes sense to disable nitogen atoms from being acceptors per default. I don't think having nitrogen acceptors is very common. Thank you in advance. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] scalar correlation matrix
Hi, Check out the modified g_covar version with correlations, which is on the user contributions. Ran. sheerychen wrote: Hello, everyone, Do anybody knows how to calculate the scalar correlation matrix across the alpha carbon atoms, where the correlation function is defined as: Cij=delta_ri*delta_rj/squart(delta_ri^2delta_rj^2). Is there any direct command can do this in gromacs? Thanks. // // ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] copper cluster bond to histidines
Dear Andrea,
Which restraints did you use?
I've ran simulations on a similar system (Zn2+ coordinated to
histidines) with NMR restraints as implemented in Gromacs and it worked
fine.
Best regards,
Ran.
andrea spitaleri wrote:
Dear all,
I am going to run some MD simulation of a protein bearing a copper cluster (3
Cu2+ nominally charge
2+) coordinates to histidine residues. As far as concerning the importance of
this cluster in the
enzymatic activity (this would require QM/MM), my issue is how to interpret
the whole system
[HIS_{2}-Cu2+]_{3} in term of force field. From literature and from previous
posts in this mailing
list, in MD system similar to mine (aminoacid coordinating ions) are treated
as an unique residues
(i.e. HEME group). My first try was to perform MD without restraints on Cu2+,
but unfortunately at
100K (I am doing an equilibration from 100K to 300K) after few ps one of the
Cu2+ left already its
position (basically it is flying away).
Second try was to put restraints on the system between the Cu2+ and the
N-HIS. However, my doubt is
how bad is this assumption respect to the possibility to consider the whole
system Cu2+-HIS as an
unique residue in the topology file. I am aware that for the latest
hypothesis I should reconsider
all the properties (i.e. charges, angles, etc ...), so a long way and hard
work. Think about that I
need to put a O2 molecule inside of the Cu2+ cluster in a second study.
Any suggestion, comments and anything else are very welcome.
Thanks in advance
Regards
andrea
--
--
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-639
Email: r.fried...@bioc.unizh.ch
Skype: ran.friedman
--
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Re: [gmx-users] Switch - Shift function electrostatics
David van der Spoel wrote: Emanuel Peter wrote: Dear Gromacs-users, At the moment I have a question which regards the different electrostatic algorithms mentioned in the Gromacs-manual. I did some simulations and I tried three different electrostatic algorithms: Cut-off, Shift and PME. It is clear to me what Shift and PME means principally, but I ask myself which electrostatic algorithm is used by Cut-off. I know that Cut-off means a twin-range-electrostatics calculation with rlist as the first range and r_coulomb as the second range. Both are calculated within different frequencies. Is that true ? In my .log file it is mentioned that when using Cut-off a default value r_coulombswitch equal to 0 is set. It is the same in the case of r_vdwswitch. Does that mean that I use in this special case a switch function which switches at 0 nm which represents in this case a shift-function that shifts my electrostatic potential in such a way, that it decays to zero at r_coulomb? I think this means that I used a shift-function which is calculated within the twin-range-electrostatics scheme. Is this true? What disadvantages does the twin-range-electrostatics calculation have in comparison to PME? Is it true that PME could stabilize my system artificially? No, it is the other way around. Cut-offs are bad. Check: J. Chem. Theor. Comp. 2 pp. 1-11 (2006) Now another question: Some people who perform molecular-dynamics calculations are stabilizing the dihedral angles in the forcefield to avoid 'unrealistical' fluctuations of their protein. Is this a reasonable way to simulate a protein? No, you are changing the force field in that way. I haven't heard of this previously. I guess you mean CMAP in CHARMM. You can check out the relevant paper, which also includes details about some other force fields. Ran. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Some questions on Tabulated Dihedral Potential
Hi Johannes, Thanks for the correction - you're right of course (when deltaX = 1 it's the same). To be closer to the gromacs code it's der = (y[N+1] - y[N-1]) * 0.5 * tabscale where tabscale = number of points per nm (or degree for angles/dihedrals). Ran. Johannes Kamp wrote: Hi Ran, are you sure the derivative is calculated as: der = (y[N+1] - y[N-1]) * 0.5 * deltaX and not as: der = (y[N+1] - y[N-1]) * 0.5 / deltaX ? The last calculation makes a little more sense to me... -Johannes Ran Friedman wrote: Hi, The numerical derivative for the Nth value y[N] is calculated as: der = y[N+1] - y[N-1] * 0.5 * deltaX Correction: der = (y[N+1] - y[N-1]) * 0.5 * deltaX where y is the potential deltaX is the difference between two successive values in your input (e.g., 1 if you have a table that goes from -180 to 180 with 361 values). I don't think you can print the number without changing the code, but it's not difficult to calculate. You can plot your forces and -der and see where they deviate. Ran. ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Some questions on Tabulated Dihedral Potential
Hi, Johannes Kamp wrote: Hi Cynthia, I'm also working on including some tabulated functions but I don't have any simulation yet. Thus I'm not a 'specialist' in this topic, but I hope I can help you a little. Dear all, I tried to include 2 tabulated dihedral potential functions into my simulation. But it seems to be not able to generate correct results. The system just exploded. I defined 3601 points in each table (from -180 to 180 with an increment 0.1). After 'mdrun', GOMACS generates two warning information: WARNING: For the 3598 non-zero entries for table 0 in table_d1.xvg the forces deviate on average 193% from minus the numerical derivative of the potential WARNING: For the 3598 non-zero entries for table 0 in table_d2.xvg the forces deviate on average 193% from minus the numerical derivative of the potential Do these two warnings matter very much? I checked the values for x,f(x),-f'(x) in the tables and don't think there're mistakes. has anyone of you met with such problems? In the tables you should supply potentials and forces. The forces are also calculated numerically, and a warning is emitted if the numerical derivatives deviate too much from the forces supplied by the user. Since the forces are interpolated, if the numerical derivative is too far from the input what you'd get will be different then expected. You can calculate the derivatives yourself and see where there are deviations. Good luck, Ran ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: 回复： [gmx-users] Re: Some questio ns on Tabulated Dihedral Potential
Hi, The numerical derivative for the Nth value y[N] is calculated as: der = y[N+1] - y[N-1] * 0.5 * deltaX where y is the potential deltaX is the difference between two successive values in your input (e.g., 1 if you have a table that goes from -180 to 180 with 361 values). I don't think you can print the number without changing the code, but it's not difficult to calculate. You can plot your forces and -der and see where they deviate. Ran. hong bingbing wrote: Hi, Ran, The potential f(x) and force -f'(x) in the table are calculated by myself before constructing the table. The potential can be written in an analytical form and the force is calculated as the analytical negative derivative of the potential at point x. There should not be so large deviation betw. the value I supplied and the value calculated by GROMACS. Wait. Is there something wrong in my interpretation? What's your method to get the force? Is there a way to see the numerical derivative generated by GROMACS? Thanks CH ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: 回复： [gmx-users] Re: Some questio ns on Tabulated Dihedral Potential
Ran Friedman wrote: Hi, The numerical derivative for the Nth value y[N] is calculated as: der = y[N+1] - y[N-1] * 0.5 * deltaX Correction: der = (y[N+1] - y[N-1]) * 0.5 * deltaX where y is the potential deltaX is the difference between two successive values in your input (e.g., 1 if you have a table that goes from -180 to 180 with 361 values). I don't think you can print the number without changing the code, but it's not difficult to calculate. You can plot your forces and -der and see where they deviate. Ran. hong bingbing wrote: Hi, Ran, The potential f(x) and force -f'(x) in the table are calculated by myself before constructing the table. The potential can be written in an analytical form and the force is calculated as the analytical negative derivative of the potential at point x. There should not be so large deviation betw. the value I supplied and the value calculated by GROMACS. Wait. Is there something wrong in my interpretation? What's your method to get the force? Is there a way to see the numerical derivative generated by GROMACS? Thanks CH ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: 回复： 回复： [gmx-users] Re: So me questions on Tabulated Dihedral Potential
As I wrote it der is the derivative itself, so you should plot (-1)*der. Ran. hong bingbing wrote: Thanks Ran. Should there also be a minus sign before (y[N+1]-y[N-1]) because the third column in the table is -f'(x)? CH *发件人：* Ran Friedman r.fried...@bioc.uzh.ch *收件人：* Discussion list for GROMACS users gmx-users@gromacs.org *已发送：* 2009/7/21(周二), 上午9:41:42 *主题：* Re: 回复： [gmx-users] Re: Some questions on Tabulated Dihedral Potential Ran Friedman wrote: Hi, The numerical derivative for the Nth value y[N] is calculated as: der = y[N+1] - y[N-1] * 0.5 * deltaX Correction: der =聽 (y[N+1] - y[N-1]) * 0.5 * deltaX where y is the potential deltaX is the difference between two successive values in your input (e.g., 1 if you have a table that goes from -180 to 180 with 361 values). I don't think you can print the number without changing the code, but it's not difficult to calculate. You can plot your forces and -der and see where they deviate. Ran. hong bingbing wrote: Hi, Ran, The potential f(x) and force -f'(x) in the table are calculated by myself before constructing the table. The potential can be written in an analytical form and the force is calculated as the analytical negative derivative of the potential at point x. There should not be so large deviation betw. the value I supplied and the value calculated by GROMACS. Wait. Is there something wrong in my interpretation? What's 聽your method to get the force? Is there a way to see the numerical derivative generated by GROMACS? Thanks CH ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- 好玩贺卡等你发，邮箱贺卡全新上线！ http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] indexing largest cluster with g_clustsize
Hi Dmitri, It's the last frame - the file is written after all frames are read and dealt with. Best regards, Ran Dmitri Dubov wrote: Dear gmx'ers! One more question on g_clustsize routine: It produces an index file with the atom numbers of largest cluster. But how it works in an evaporating system where the number of clustered molecules reduces greatly through the trajectory? What frame the maxclust.ndx file concerns to? -- Regards Dmitri mailto:ddu...@ngs.ru ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Department of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-639 Email: r.fried...@bioc.unizh.ch Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] xdr library. Just for an example.
Hi Vitali, There should be such code with then library itself. Ran. Vitaly V. Chaban wrote: Hi, Can anybody share any working code which uses xdr-1.1 library? - Just to consult. Thank you very much in advance, Vitaly ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] lincs warning
Hi XAvier, Do you use virtual sites? I've seen this when I used virtual sites, large time steps and a system that probably wasn't equilibrated enough. Ran. XAvier Periole wrote: Dears, I am experiencing some problems running a few proteins in water (GROMOS43a1/SPC) with gmx-4.0.4 using 32 CPUs. After some ns lincs warnings appear and eventually the simulation crashes dues to too many lincs warnings. When restarting the simulation feeding -cpi md.cpt to mdrun the simulation restarts fine and no lincs warning are reported on the same portion of the simulation. The simulation runs again for some ns and the same happens: new lincs warning appear and eventually the simulation crashes again. Any explanation for this? Any solution? Best, XAvier. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] oplsaa parametrization
R. A. wrote: Dear Users I m trying to simulate a structure (not a protein) which is not parametrized in oplsaa FF. I created the structure using PRODRG and included the results of *.itp from PRODRG to ffoplsaa.rtp file and tried to use available oplss_xxx for my atom type near to those ones already exists in *.atp. I also optimized my structure at RHF/6-31G* level and calculated the charge using resp. Then updated ffoplsaa.rtp using this calculated charge. By refering to the mailing list it seems that I need to modify bn.itp and nob.itp file as well (?!). I m just wonder if anybody use PRODRG how he/she parametrized FF. As I m new in GROMACS and any tutorial or procedure to follow will help me so much. Thank you in advance for any ideas or comments. As far as I know PRODRG doesn't produce itp files comparable with OPLS, so you need to use something else or manual modifications. Ran. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] oplsaa parametrization
Hi Rosa, You can read the paper on PRODRG to study how they parametrise. There's a topology builder for OPLS-AA: http://labmm.iq.ufrj.br/mktop/ There're also commercial tools (see some previous posts on the mailing list) and you can also start with PRODRG and modify the files to have the right parameters as in GMX. However, you should verify that your molecules are correctly parametrised no matter what software you're using - run a simulation with it and see if things look all right (e.g., if rings are not too distorted, bonds are correct etc.) and try to get experimental parameters to compare with. It has been stressed out a lot in the list that this is an advanced issue - being familiar with MD and the FF you're using is a pre-requisite to parametrisation. Good luck, Ran. Dear Ran Thanks for the reply. I think I `ve read some papers using PRODRG and opls. However they didnt mention clearly that how they parametrized their force field. Just do you know any alternative software. As I checked many softwares but I couldnt find any to create .itp file at the same time. Thank you. Regards Rosa -- Be Yourself @ mail.com! Choose From 200+ Email Addresses Get a *Free* Account at www.mail.com http://www.mail.com/Product.aspx! ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: MD with RMSD restraint
Hi, You can also use essential dynamics sampling. Ran. David van der Spoel wrote: Sam Moors wrote: Hi, Position restraints do not allow me to do what I want. For instance, I want to allow the system to freely explore the conformational space within a certain RMSD range, but not evolve beyond a specified RMSD cutoff. Another application would be to push the system conformation away from the reference structure, by using negative force constants. Therefore the reference structure should be fitted to the simulation structure (or the other way around) before calculating the position differences. Then you have to derive a force that is the derivative of the RMSD with respect to the positions. This may be difficult, since you have the superposition step in between. What you could do straight away is move from normal RMSD to distance-based RMSD, in which case the this has been implemented using distance restraints. You would use genrestr to generate the additional topology input, then determine a suitable force constant and Bob's your uncle. Cheers. Thanks in advance for your help, Sam Mark Abraham wrote: Sam Moors wrote: Hi gmx users/developers, I would like to do a molecular dynamics simulation with a restraint on the backbone RMS deviation from a reference structure. Does anybody know if this is possible? How about position restraints only on the backbone? Same effect. Not exactly as you describe, but you should read the section in chapter 4 of the manual and see for yourself. If yes, could you explain how to do it? If no, what would be the easiest way to implement this in gromacs? It could be done, but I'm not sure it's worth the effort. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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. sp...@xray.bmc.uu.sesp...@gromacs.org http://folding.bmc.uu.se -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 61, Issue 77 * ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] different result for entropy with normal mode analysis and schlitter-approximation
Hi Oliver,
I think the eigenvalues in NMA are not the same (there used to be a
factor of 2PI and the mass weighting). Maybe you can try my script from
the user contributions and see if you get something more reasonable (use
to flag -n to indicate that your eigenvalues are from NMA).
Ran.
oliver.k...@uni-duisburg-essen.de wrote:
Dear Gromacs Users,
I'm trying to calculate entropies from a md trajectory using g_anaeig.
There are two ways to go (question at bottom ;-):
1. NMA and quasi-harmonic approximation: Use a bunch of snapshots (maybe
5-20), minimize each of them to very low maximum forces, calculate the
hessian matrix, diagonalize and use g_anaeig to calculate the entropy from
the resulting eigenvector-matrix assuring that there are no negative
eigenvalues in the eigenvectors 7 to N (first six eigenvectors will not be
part of the calculation). - as follows:
# Energy Minimization
grompp_d -f em_nma.mdp -t md.fitted.trr -time $t -c md.gro -p protein.top
-o $t.em.tpr
mdrun_d -v -deffnm $t.em -table table6-12_4r_doublePrecision.xvg -tablep
table6-12_4r_doublePrecision.xvg
# Hessian Matrix
grompp_d -f nma.mdp -t $t.em.trr -c md.gro -p protein.top -o $t.hessian.tpr
mdrun_d -v -deffnm $t.hessian -table table6-12_4r_doublePrecision.xvg
-tablep table6-12_4r_doublePrecision.xvg
# Diagonalization of the Hessian
g_nmeig_d -f $t.hessian.mtx -s $t.hessian.tpr -first 1 -last 1 -v
$t.eigenvec.trr
# Entropy calculation - vibrational (without first 6 modes)
g_anaeig_d -v $t.eigenvec.trr -f $t.em.trr -s $t.hessian.tpr -temp 298.15
-nevskip 6 -entropy 21 | tee out.anaeig.Svib.$t
grep 'The Entropy due to the Quasi Harmonic approximation is'
out.anaeig.Svib.$t | awk '{print $10}' result/Svib.nma
I use distance-dependent dielectric e=4r, but that doesn't make much
difference.
2. Schlitter approximation based on covariance: Use all snapshots of the
md trajectory, calculate the covariance matrix (g_covar), - diagonalized
matrix will be returned -, and subsequently calculate the entropy with
g_anaeig. - as follows:
# covariance matrix as time average over configurations
g_covar_d -f md$i.trr -s md.gro -v md$i.eigenvec.trr -mwa -av
average.$i.pdb -ascii covar.$i -xpm covar.$i -xpma covara.$i -l covar.$i
-o md$i.eigenval.xvg - EOF
0
0
EOF
# Analysis of the principal components (and entropy calculation)
g_anaeig -v md$i.eigenvec.trr -f md$i.trr -s md.gro -first 1 -last -1
-entropy out.anaeig.schlitter.$i
grep 'The Entropy due to the Schlitter formula is' out.anaeig.schlitter.$i
| awk '{print $9}' result/Svib.schlitter
Somebody before mentioned, he would like to have the undiagonalized
covariance matrix as input for the entropy calculation, I think, that
doesn't make a difference, am I right?
So, practically, I tried to reproduce entropy from Schlitter 1993. A
simulation of a deca-alanine-helix in vacuo in the old gmx force-field
with vdw-cut-off etc. and I could reproduce the value of ca. 700
kJoule/mol K with the Schlitter approximation.
And now the question, why don't I get the same range of values when doing
normal-mode analysis (as described above)?
values of the Schlitter-approximation (for different simulation lengths):
667.365
685.594
681.259
680.269
values given by the quasi-harmonic approximation when calculating from
covariance:
582.731
596.97
590.71
589.07
values from NMA and quasi-harmonic approximation (for 3 snapshots):
21662.9
21674.9
21662.9
So, there is a factor of round 30 between hessian- and covariance-based
entropy!?
I'm totally stuck with this.
If anybody has experience with this phenomenon, any help is appreciated.
Thanx in advance
Oliver Kuhn
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--
--
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: r.fried...@bioc.unizh.ch
Skype: ran.friedman
--
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Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones
Dear Josmar, As for the GROMOS FF, I've included a link to the paper describing the most recent (AFAIK) version of the FF in one of the recent mailing list massages. Good luck, Ran On Sat, 18 Apr 2009 15:56:11 -0400 Justin A. Lemkul jalem...@vt.edu wrote: Josmar R. da Rocha wrote: Dear Ran, Thanks for answering and sorry to take so long to reply. After your response I went seach for more information about that. What I read here in the list is that some people uses antechamber to generate am1-bcc charges (or RESP charges using Gaussian program) and convert the output files to a .top file (using the amb2gmx.pl script) that can be used in gromacs, however, nobody says the kind of ff they intend to use that charges with. Do these type of charges can also be used with Gromos96 ff ( 43a1)? Thanks in advance! The amb2gmx was created to handle AMBER-to-GROMACS conversion. It is unlikely that it would be useful for ffG43a1. Since 43a1 is a united-atom force field, you have to compensate for the fact that nonpolar hydrogen atoms are absent. Furthermore, quantum charge calculation is not a necessary component of Gromos96 parameter derivation. See, for example: http://wiki.gromacs.org/index.php/Parameterization -Justin Regards, Josmar Rocha --- Em *sex, 27/3/09, Ran Friedman, Biochemisches Inst. /r.fried...@bioc.uzh.ch/* escreveu: De: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch Assunto: Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones Para: bije...@yahoo.com.br, Discussion list for GROMACS users gmx-users@gromacs.org Data: Sexta-feira, 27 de Março de 2009, 17:35 Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with the same chemical moieties or use the same approach as reported in the relevant manuscripts. Some software packages can also be used - these are mostly proprietary and not so easy to use. Once you derive the parameters, it's a good idea to make some test runs of the ligands and see if they behave as expected before you actually run a simulation with the protein. For example, if a conjugate ring system isn't planar something may be wrong in the setting. There's no easy solution - this is why it's considered an advanced topic. It is, however, very important. I've encountered a ligand that leaves its binding site during a simulation due to wrong parameters (in this case, the protonation of a protein side chain - FEBS 581, Pages 4120-4124, 2007). Hope that helped, Ran On Fri, 27 Mar 2009 12:22:01 -0700 (PDT) Josmar R. da Rocha bije...@yahoo.com.br wrote: Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. Verli pointed out the use of semi-empirical methods such as RM1 in cases not involving simulations with sulphate or phosphate groups (what is not my case) and the use of QM methods with the 6-31G** basis set, for example, to obtain robust charges (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the other hand Dr. Mobley defined as a a bad idea to compute charges for an all-atom case using QM and then try to convert these to a united atom force field. Other users advice that the best charges are that compatible with the force field parametrization (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman suggested that to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential in order to make it less sensitive to small changes in the geometry of the molecule may give good results (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. Lemkul stressed the need for charges refinement to reproduce experimentally-observed behavior while trying to use QM charges with Gromos ff. since Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. Few examples of protein-ligand studies using Gromacs and Gromos96 ff that I have access (from literature) seem to treat it as take
Re: [gmx-users] the vdw and electrostatic energy
Hi, This problem has been discussed for decades in the literature. There are approaches such as PME and reaction field to deal with the long-range electrostatics. Ran. Dechang Li wrote: Dear all, When we do a MD simulation, we always set a cutoff of non-bonded interactions, e.g. r=1.2 nm. When the simulation finished, we can use the command g_energy -f ener.edr -s ... to abtain the non-boned energy of the system. My question is whether the non-bonded energy values dependent on the non-bonded cutoff? If YES, there may be no problem of the vdw interaction (LJ-SR), because the vdw interaction vanish in a short distance. But how about the electrostatic term with the distance dependence of 1/r^2 ? Best regards, = Dechang Li, Ph.D Candidate Department of Engineering Mechanics Tsinghua University Beijing 100084 P.R. China Tel: +86-10-62773574(O) Email: lidc02 at mails.tsinghua.edu.cn = ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- 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: r.fried...@bioc.unizh.ch Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re:Re: the vdw and electrostatic energy (Ran Friedman)
No. SR stands for short-range. Ran. I did not mean that. I want to know that when we use g_energy in Gromacs to read the energy from the file ener.edr, does the cutoff affect the values of the energy? For example, when the cutoff is set to 1.2 nm and the PME method is used, does the energy term Coul-SR read by g_energy contain the long range part ? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Topologies and charges for large organic ligands
Hi,
The answer is (or should be) in:
@article{Oostenbrink2004,
Author = {Oostenbrink, C. and Villa, A. and Mark, A. E. and Van
Gunsteren, W. F.},
Title = {A biomolecular force field based on the free enthalpy of
hydration and solvation: The GROMOS force-field parameter sets 53A5 and
53A6},
Journal = {J. Comput. Chem.},
Volume = {25},
Pages = {1656-1676},
Year = {2004} }
Good luck,
Ran.
Dean Cuebas wrote:
Dear colleagues,
In 53a6, the topology and charges for (NAD+) nicotinamide adenine
dinucleotide are present (listed as NADH, 52 atoms) in polar hydrogen form
(without aromatic hydrogens).
Is there anyone who can tell me how such a molecule was charge group
parameterized? (with sufficient certainty to be included in the ff).
Please understand that I am not asking how to use the NAD topology that's
provided.
I've read that prodrg is a good starting point for parametrizing a ligand,
but what is the path to improving such a ligand from that starting point?
(the provided topology for NAD+ in the ff shows 17 charge groups with
an average of 3-4 atoms per charge group, whereas prodrg gives only 11
charge groups.)
I'm not concerned about angles and dihedrals, since that is pretty
painless... it's the charge groups that I'm concerned about.
In a nutshell, who and how was the final NAD+ parameters decided upon??
Does anyone know this?? Is it simply chemical intuition of estimated
charges that reproduce the dipole of the moiety (like an adenine ring), and
the charge groups contain the minimum number of atoms that reflect this?
Is there an algorithm to generating improved charge groups?
I ask these questions because my ligands are large organics... MW 800 and
greater.
Thanks for any and all help in this regard.
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Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones
Hi, I've recently used OPLS-AA for a similar calculation. It has the advantage that many atom types are already defined in Gromacs and that QM-based calculations give you reasonable charges. Note that it may take considerable simulation time (tens of ns) to discriminate between similar docked poses of the same molecule, though MD can give you a hint. If things were easier docking programs would do a better job. Ran. On Wed, 01 Apr 2009 00:12:31 -0600 Lucio Ricardo Montero Valenzuela lucio...@ibt.unam.mx wrote: So it 's better to switch to the OPLS forcefield if I want to compute the charges?. How can I implement the OPLS-UA if my gromacs (version 3.3) only includes the OPLS-AA? Mensaje citado por Justin A. Lemkul jalem...@vt.edu: Lucio Montero wrote: How about MOPAC to calculate the charges for 3-methyladenine (this molecule has a charge +1) for using the G43a1 force field?. That may not be a bad place to start, but any parameters applied to a Gromos molecule have to reproduce condensed phase thermodynamic observables. Empirical fitting of the initial parameters may be required. Refer to the primary literature. The reference for the 53a5 and 53a6 parameter sets are published in JCC, which may provide you with some useful information. -Justin -- From: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch Sent: Friday, March 27, 2009 2:35 PM To: bije...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRGassignedones Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with the same chemical moieties or use the same approach as reported in the relevant manuscripts. Some software packages can also be used - these are mostly proprietary and not so easy to use. Once you derive the parameters, it's a good idea to make some test runs of the ligands and see if they behave as expected before you actually run a simulation with the protein. For example, if a conjugate ring system isn't planar something may be wrong in the setting. There's no easy solution - this is why it's considered an advanced topic. It is, however, very important. I've encountered a ligand that leaves its binding site during a simulation due to wrong parameters (in this case, the protonation of a protein side chain - FEBS 581, Pages 4120-4124, 2007). Hope that helped, Ran On Fri, 27 Mar 2009 12:22:01 -0700 (PDT) Josmar R. da Rocha bije...@yahoo.com.br wrote: Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. Verli pointed out the use of semi-empirical methods such as RM1 in cases not involving simulations with sulphate or phosphate groups (what is not my case) and the use of QM methods with the 6-31G** basis set, for example, to obtain robust charges (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the other hand Dr. Mobley defined as a a bad idea to compute charges for an all-atom case using QM and then try to convert these to a united atom force field. Other users advice that the best charges are that compatible with the force field parametrization (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman suggested that to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential in order to make it less sensitive to small changes in the geometry of the molecule may give good results (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. Lemkul stressed the need for charges refinement to reproduce experimentally-observed behavior while trying to use QM charges with Gromos ff. since Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. Few examples of protein-ligand studies using Gromacs and Gromos96 ff that I have access (from literature) seem to treat it as take it for granted issue (any reference with a more detailed description would be welcome :-)). Despite reading on this topic I could not compile all the information in a clear and objective way (may be because I'm in the wrong track). Let ask you some question
Re: [gmx-users] HF/6-31G** ESP derived charges to replace PRODRG assigned ones
Dear Josmar, You haven't written which force field you plan to use. For OPLS and AMBER QM-based optimisation should be fine. In Gromos, the FF was developed with the aim of reproducing experimental results and I'm not sure if you can find a better solution than examining other residues with the same chemical moieties or use the same approach as reported in the relevant manuscripts. Some software packages can also be used - these are mostly proprietary and not so easy to use. Once you derive the parameters, it's a good idea to make some test runs of the ligands and see if they behave as expected before you actually run a simulation with the protein. For example, if a conjugate ring system isn't planar something may be wrong in the setting. There's no easy solution - this is why it's considered an advanced topic. It is, however, very important. I've encountered a ligand that leaves its binding site during a simulation due to wrong parameters (in this case, the protonation of a protein side chain - FEBS 581, Pages 4120-4124, 2007). Hope that helped, Ran On Fri, 27 Mar 2009 12:22:01 -0700 (PDT) Josmar R. da Rocha bije...@yahoo.com.br wrote: Dear users, I have been reading some posts about using externally computed charges to replace Prodrg charges at ligand topology files. Many users commented on the low trustability given to Prodrg charges (e.g http://www.mail-archive.com/gmx-users@gromacs.org/msg02360.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg17351.html ). Dr. Verli pointed out the use of semi-empirical methods such as RM1 in cases not involving simulations with sulphate or phosphate groups (what is not my case) and the use of QM methods with the 6-31G** basis set, for example, to obtain robust charges (http://www.mail-archive.com/gmx-users@gromacs.org/msg03410.html). On the other hand Dr. Mobley defined as a a bad idea to compute charges for an all-atom case using QM and then try to convert these to a united atom force field. Other users advice that the best charges are that compatible with the force field parametrization (http://www.mail-archive.com/gmx-users@gromacs.org/msg10760.html ; http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html), usually pointing to http://wiki.gromacs.org/index.php/Parameterization. Dr Friedman suggested that to calculate the electrostatic potential over the whole molecule, and fit the atomic charges so that they reproduce this potential in order to make it less sensitive to small changes in the geometry of the molecule may give good results (http://www.mail-archive.com/gmx-users@gromacs.org/msg08308.html). Dr. Lemkul stressed the need for charges refinement to reproduce experimentally-observed behavior while trying to use QM charges with Gromos ff. since Parameterization under Gromos usually involves empirical derivation of physical parameters, and free energy calculations using thermodynamic integration. Few examples of protein-ligand studies using Gromacs and Gromos96 ff that I have access (from literature) seem to treat it as take it for granted issue (any reference with a more detailed description would be welcome :-)). Despite reading on this topic I could not compile all the information in a clear and objective way (may be because I'm in the wrong track). Let ask you some question that I find would help me to make my ideas more clear: 1-am I overestimating the importance of ligand charges in such a simple study of protein-small molecule (containg charged Phosphate groups) complex? or 1.1-The only way to test for this is doing many different simulation on the same system using different type of computed charges to see what happen? 2-How could I try to choose a method to obtain reasonable charges based on the reproduction of experimentally-observed behavior if I do not have experimental data for my system? 3-I also would like to know from users dealing with protein-ligand interactions studies what do you consider a good approach to address this problem? Based on what I read I'd have a tendency to use HF/6-31G** ESP derived charges (with necessary changes as to make it united-atom charges and scaling that to a integer number for each group). Please, let me know if that strategy would be as good as a disaster! Thank you very much for the attention. Josmar Rocha Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Using R.E.D. charges with OPLS AA
Hi,
HF with 6-31G usually provide a good start for getting OPLS charges:
@article{Jorgensen1996,
Author = {Jorgensen, W. L. and Maxwell, D. S. and Tirado-Rives, J.},
Title = {Development and Testing of the {O}{P}{L}{S} All-Atom Force
Field on
Conformational Energetics and Properties of Organic Liquids.},
Journal = {J Am Chem Soc},
Volume = {118},
Pages = {11225-11236},
Year = {1996} }
How you assign your charges to the molecule is another issue. I normally
fit the partial charges to the electrostatic potential around the
molecule. RESP was indeed developed with AMBER, but I don't know if the
charges are so different.
Good luck,
Ran
DimitryASuplatov wrote:
Hello,
I need to simulate a protein with deprotonated Tyr (HH hydrogen should
be off). I used R.E.D. approach with PCGAMESS and RESP to calculate the
charges.
1/ The problem is that to my understanding RESP charges apply to AMBER
only. Am I correct?
2/ Can I use R.E.D. charges with OPLS AA?
3/ If not how can I recalculate them to fit the OPLS AA?
4/ Any Tyr-Deprot topology already available???
Thanks, I appreciate your time.
SDA
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--
--
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: r.fried...@bioc.unizh.ch
Skype: ran.friedman
--
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[gmx-users] Re: g_covar
Dear Dagoberto, Choosing the right protein structure (and also which part of the protein to align) depends a lot of your system. I wouldn't use an average structure for a system that's changing a lot, because it may not be representative. It's hard to provide a more elaborate answer without many details about your system and what you're trying to simulate. It can be helpful to read both on the methods of covariance analysis and on some implementation - i.e., papers in which it has been used to calculate correlated motion. As to modification of the code, I found it easiest to compile the source code for various tools within GMX. It's not necessary, but it makes your life easier. Since your question doesn't refer to the modified g_covar code directly, I'm ccing the gromacs mailing list. Please keep future correspondence there. Good luck, Ran darme...@ibt.unam.mx wrote: Dear Ran friedman I'm actually biochemistry student and I'm using your uploaded version of g_covar in order to calculate correlated motion. I have c-alpha trajectory of 50 ns simulation that describe the functional movement of my protein, but the trajectory are not in the equilibrium. My questions are, what reference structure I must use in order to calculate correlated motion?, could I use the average structure as reference? In the other hand, Im doing some modifications to the g_covar program and I want to know the way to compile it. Is necessary to compile within gromacs? What is the easiest way? I would appreciate any help in this matter. Dagoberto Armenta Medina Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs 4 mpi weirdness
shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes configure: creating libtool appending configuration tag CXX to libtool appending configuration tag F77 to libtool checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... 64 checking for _LARGEFILE_SOURCE value needed for large files... 1 checking for sqrt in -lm... yes checking for fftw3.h... yes checking for main in -lfftw3f... yes checking rpc/rpc.h usability... yes checking rpc/rpc.h presence... yes checking for rpc/rpc.h... yes checking for rpc/xdr.h... yes checking for xdr_float in -lnsl... yes checking for working memcmp... yes checking return type of signal handlers... void checking for off_t... (cached) yes checking for vprintf... yes checking for _doprnt... no checking if malloc debugging is wanted... no checking for strcasecmp... yes checking for strdup... yes checking for bool... no checking for X... libraries , headers checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking libxml/parser.h usability... yes checking libxml/parser.h presence... yes checking for libxml/parser.h... yes checking for main in -lxml2... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether struct tm is in sys/time.h or time.h... time.h checking for uid_t in sys/types.h... yes checking for inline... inline checking whether your compiler can handle assembly files (*.s)... yes checking whether as fully supports ia32 SSE... yes checking whether as fully supports ia32 3DNow! instructions... yes checking whether byte ordering is bigendian... (cached) no checking if the compiler supports gcc inline assembly... yes checking if the compiler supports MSVC inline assembly... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/gmxlib/Makefile config.status: creating src/gmxlib/gmx_blas/Makefile config.status: creating src/gmxlib/gmx_lapack/Makefile config.status: creating src/gmxlib/nonbonded/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_3dnow/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ia32_sse2/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_x86_64_sse2/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ppc_altivec/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_single/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_ia64_double/Makefile config.status: creating src/gmxlib/nonbonded/nb_kernel_bluegene/Makefile config.status: creating include/Makefile config.status: creating include/types/Makefile config.status: creating src/mdlib/Makefile config.status: creating src/kernel/Makefile config.status: creating src/tools/Makefile config.status: creating src/ngmx/Makefile config.status: creating src/contrib/Makefile config.status: creating scripts/Makefile config.status: creating admin/Makefile config.status: creating share/Makefile config.status: creating share/tutor/Makefile config.status: creating share/tutor/gmxdemo/Makefile config.status: creating share/tutor/nmr1/Makefile config.status: creating share/tutor/nmr2/Makefile config.status: creating share/tutor/water/Makefile config.status: creating share/tutor/mixed/Makefile config.status: creating share/tutor/methanol/Makefile config.status: creating share/tutor/speptide/Makefile config.status: creating share/template/Makefile config.status: creating share/top/Makefile config.status: creating share/html/Makefile config.status: creating share/html/images/Makefile config.status: creating share/html/online/Makefile config.status: creating man/Makefile config.status: creating man/man1/Makefile config.status: creating src/config.h config.status: executing depfiles commands * On most platforms you can save 10X space with dynamic libraries, although the binaries might be less portable. Why not try --enable-shared ? -- -- 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: r.fried...@bioc.unizh.ch Skype: ran.friedman
Re: [gmx-users] initial velocities Langevin dynamics
Hi Loris,
It may be better to have ld_seed=-1. This way, you won't have the same
seed again when you restart.
@Article{Cerutti2008,
author = Cerutti, D S and Duke, R and Freddolino, P L and Fan, H and
Lybrand, T P,
title = {Vulnerability in Popular Molecular Dynamics Packages Concerning
Langevin and Andersen Dynamics},
journal = J Chem Theory Comput,
year = 2008,
volume = 4,
pages = 1669-1680
}
Best regards,
Ran
Loris Moretti wrote:
Dear Mark and Oscar,
Thanks for your help!
I checked the velocity distribution and the velocity at different simulation
frames. As you said the initial velocities are all set to zero and at the
next step are already changed, I also guess by the random thermal noise.
Thus, my idea of simulating the same system with different random generator
number for thermal noise (ld_seed) might account for a small variation of the
initial conditions?
loris...
In message 8c3f24a40903110611j4f69c75emb0f5eef0484de...@mail.gmail.com
Discussion list for GROMACS users gmx-users@gromacs.org writes:
Thus I am a bit confused about it!
I'm confused about the manual comment about only being meaningful with the
MD integrator, but we 'll have to wait until someone who knows something
about LD can post!
For LD, the velocities will (should) get rescaled by the random thermal
noise, that is- by the Langivin thermostat.
With MD, the thermostat works like friction (positive or negative friction).
So you see, that for LD, an initial velocity of zero should next be changed
by the thermostat, while for MD the rescaling shouldn't work for zero.
--Omer Markovitch.
Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] Conversion of trajectories to netcdf format
I don't know about netcdf, but you can use wordom to convert from xtc to dcd. Contact me off list if you don't succeed - I'm not sure whether the online documentation of wordom is up-to-date. Ran. Tobias Unruh wrote: Hi, I would like to use nMolDyn for the analysis of the GROMACS trajectories. I tried VMD and catdcd to convert trr/tpr files to dcd/pdb files. But the conversion of the dcd/pdb files to nc (netcdf) files using the dcd_to_nc program of the nMolDyn package does not work. Obviously the header of the dcd file differs from what is expected by the dcd_to_nc program which uses MMTK. Does anyone know how to convert the GROMACS trajectories such that nMolDyn can be used for calculation of correlation and intermediate scattering functions? I appreciate any suggestion. Regards Tobias -- Tobias Unruh TU Muenchen, FRM-II 85747 Garching, Germany ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- 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: r.fried...@bioc.unizh.ch Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] gromacs 4.0.3 tests validations
Hi, I think the tests for pdb2gmx are outdated. Most fail due to warning(s) while running grompp, which were allowed with older versions. I'm not sure who maintains this tests - maybe a new version is due. Ran. Tru Huynh wrote: Hi, I am compiling gromacs on CentOS-3 x86_64 both serial and LAM-MPI version (7.1.4) and I would like to validate the builds. [...@sillage gmxtest]$ rpm -q gcc fftw3 perl gcc-3.2.3-59.x86_64 fftw3-3.0.1-2_centos3.x86_64 perl-5.8.0-98.EL3.x86_64 ./configure --prefix=... --with-x --enable-shared make make install test validation as stated at http://wiki.gromacs.org/index.php/Test-set wget -O - ftp://ftp.gromacs.org/pub/tests/gmxtest-3.3.2.tgz| tar xzvf - make tests ... All 16 simple tests PASSED All 14 complex tests PASSED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file - The PASSED lines are fine to me, but what about the last 2 lines? I also compiled the double precision version with: ./configure --prefix=... --with-x --enable-shared --disable-float and the tests yields: [...@sillage gmxtest]$ ./gmxtest.pl -double all All 16 simple tests PASSED All 14 complex tests PASSED All 63 kernel tests PASSED readline() on closed filehandle PIPE at ./gmxtest.pl line 343. readline() on closed filehandle PIPE at ./gmxtest.pl line 348. ... readline() on closed filehandle PIPE at ./gmxtest.pl line 348. readline() on closed filehandle PIPE at ./gmxtest.pl line 343. readline() on closed filehandle PIPE at ./gmxtest.pl line 348. Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file Should I be worried? About the parallel test (grompp -np N for gromacs 3.x) as previoulsy stated on the mailing list, one should use: grompp -c system.gro -p topology.top -f something.mdp mpirun -np N mdrun so gmxtest.pl should read: system($grompp -maxwarn 10 $ndx /dev/null 21); system(mpirun -$par mdrun -maxwarn 10 $ndx grompp.out 21); instead of: system($grompp -maxwarn 10 $ndx $par grompp.out 21); [...@sillage gmxtest]$ ./gmxtest.pl -np 1 all Will test on 1 processors All 16 simple tests PASSED All 14 complex tests PASSED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file [...@sillage gmxtest]$ ./gmxtest.pl -np 2 all Will test on 2 processors FAILED. Check files in bham 1 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in aminoacids FAILED. Check files in argon FAILED. Check files in sw FAILED. Check files in tip4p FAILED. Check files in urea FAILED. Check files in water 7 out of 14 complex tests FAILED All 63 kernel tests PASSED Error not all 45 pdb2gmx tests have been done successfully Only 0 energies in the log file Thanks. Tru ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Barostat Density decreasing to zero
Hi Omer, You use a dielectric constant is 80, which means that the electrostatic interactions are screened. Perhaps that's why your density is low. Ran. Omer Markovitch wrote: Dear All, I have simulated a protein inside a box with water and ions. I began by minimizing my system (which has a total charge of zero), until the maximum gradient was small enough and the potential energy become negative. Then I heated it, slowly, to 300K at constant volume (using berendsen thermostat and tcoupl = 1 ps). Then I performed 500 ps NVT simulation to equilibrate the temperature, at 300K. Then, I tried to equilibrate the pressure and run NPT simulation, using Berendsen barostat (p=1, pcoupl=10) and Berendsen thermostat (T=300K, tcoupl = 0.1). My problem is, that with the barostat thermostat both active in the same MD run, my density drops to a very low value (at the first MD steps, the density is 1000, dropping later to 100 kg/m^3). That is- my box dimensions increase significantly (from around 6x6x6 to 12x12x12 nm^3. If I change the pressure coupling constant, the speed of the expansion changes but all simulation converged to a small density between 50-100 kg/m3. Your help is appreciated; Probably, I am not controlling the simulation like I should. I will appreciate any advice. Thank you, Omer Markovitch. I have used gromacs version 3.3.3, Here is my .MDP file for the NPT run: integrator = md dt = 0.001 nsteps = 50 comm_grps= system nstxout = 500 nstvout = 500 nstcheckpoint= 1000 nstlog = 500 nstenergy= 500 nstlist = 10 ns_type = simple pbc = xyz rlist= 1.0 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.0 epsilon_r= 80 epsilon_rf = 80 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1.0 table-extension = 1 fourierspacing = 0.12 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d optimize_fft = yes tcoupl = berendsen tc-grps = system tau_t= 0.1 ref_t= 300 Pcoupl = berendsen Pcoupltype = Isotropic tau-p= 10 compressibility = 4.5E-5 ref-p= 1 andersen_seed= 815131 constraints = none ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator
Hi, Maybe it's a good idea to have ld-seed=-1 as a default if that's not already the case. Ran. Berk Hess wrote: Hi, I don't know why I did not add checks for ld-seed before. Now grompp gives a note when continutation=yes and ld-seed!=-1. tpbconv will now generate a new ld-seed when reading a trajectory (but you should not use tpbconv, use a checkpoint file instead). But yesterday I forgot to tell that there is a bug in the checkpointing of mdrun in 4.0 - 4.0.3. Without domain decomposition the initial box size would always be stored in the checkpoint file, which causes problems with NPT simulations. NPT simulations with domain decomposition and all NVT simulations were fine. Gromacs 4.0.4 will all bugs fixed and extra checks should be released today. Berk Date: Wed, 4 Feb 2009 19:30:47 -0500 From: chris.ne...@utoronto.ca To: gmx-users@gromacs.org Subject: [gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator It appears as if you were correct Berk. I will report on the results of my 24h test tomorrow, but I also set up another system that used ld_seed=1993 and ran in 20 ps segments instead of the 200 ps segments that I was previously using. This system shows signs of disaggregation on the 200 ps time-scale as opposed to the 2 ns time-scale that I observed for 200 ps segments. I don't know how you figured that one out, but I am very grateful. Now that I see the trajectories, it does make sense that any net movement applied to an individual molecule by the noise will lead to directed movement over many separate segments. I think this is probably worth a note in the grompp output for sd runs when a user sets ld_seed to something other than -1 and utilizes the -t option (or some other indication that this is intended as a continuation). Chris. -- original message -- Thank you Berk, I will repeat my runs using the checkpoint file and report my findings back to this list. Thank you for this advice. Chris. -- original message -- Hi, In this manner you use the same random seed and thus noise for all parts. In most cases this will not lead to serious artifacts with SD, but you can never be sure. When checkpoints are used, you do not repeat random numbers. This also gives a difference between serial and parallel in 4.0. With serial you get exactly the same noise per atom, in parallel not, since atoms migrate from one node to another (with domain decompostion). If you do not use checkpoints, use ld_seed=-1 and do not use tpbconv. Berk ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Express yourself instantly with MSN Messenger! MSN Messenger http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] micelle disaggregated in serial, but not parallel, runs using sd integrator
Berk Hess wrote: Hi, That I have thought about and it would avoid a lot of trouble. But I have not done that, because that would lead to different run results every time you rerun grompp, which can be misleading when you are trying to assess the effects of other parameters. But maybe the first issue is more important than the second? That's how I feel. Many users may not be aware of potential artefacts. Ran. Berk ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Dear Berk, I think that g_clustsize has a similar problem. IIRC I fixed it in a similar way on my own copy. There are probably other tools that will suffer from this as well, but for g_clustsize it's important because it may deal with such groups. Same goes for trjconv, e.g., for a protein and ligand. Ran. Berk Hess wrote: Hi, Just to be sure, the pull code is producing the correct results now? The only problems should be in several analysis tools. The analysis tools have been written only with analysis of molecules or parts of molecules in mind. When you want to analyze groups that cover two molecules or more there will be pbc problems. These are not simple to fix. If the distances between all the atoms in the group are less than half a box length there is a unique COM. The procedure should be similar to what trjconv -pbc cluster does. I can try to implement this for g_traj and g_dist. Are there other tools that cause problems? Berk Date: Mon, 26 Jan 2009 17:46:26 -0500 From: fied...@umich.edu To: gmx-users@gromacs.org Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance Hi Chris, Your suggestions were helpful. Due to the nature of this problem, there were limitations in the application of the sequence of steps that you recommended. Specifically, the difference in the equilibrated structure from version 3.3.x to the calculated reference center of mass from version 4.0.x causes an unreasonable jump with constraint force calculation. Resultant bad contacts prohibit generation of a pull output file. More generally though, I believe I understand your broader point: the sensitive nature of the periodic box with respect to the pull code and possible discrepancies in the pbc treatment by various utilities, may cause confusion with the diagnostic process. The test bilayer system I created however, centered distantly from the x and y box edges, may effectively remove this set of concerns. For example, this configuration is relatively unchanged upon recentering, however it is still susceptible to the problem that is the subject of this discussion. If I can reproduce this phenomenon with a publicly available topology file, I can provide the necessary input files for inspection. Thank you again, Steve Fiedler chris.ne...@utoronto.ca wrote: Hi Steve, what I intended to suggest was actually something different (and much easier). The idea is not that you need some special system to be able to utilize the pull code, but that the pull code is correct whereas the g_dist and g_traj programs are not as good at treating pbc in the way that one desires. I suggest the following. 1. Take your original system and run the pull code for a very short simulation. Use the last line of the output to calculate the relevant displacement 2. Now use trjconv -b -e to get the last frame of the .xtc that resulted from that short MD run as a .gro file, call it final.gro. I suspect that your groups are not entirely in the same simulation box in final.gro. 3. Now make a new .ndx file from that .gro and give it a single residue that is near your binding pocket, call it R_1 4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1 for centering, call the new .gro file final_center.gro 5. Visualize final_center.gro and ensure that all of your relevant atoms are in the same image in the way that puts the minimum distance between them along a path that is entirely contained within the unit cell. If not, go back to step 3 and try making a group R_2, etc. until this process works. NOTE: you might think that giving trjconv -center the relevant groups that you use for pulling will be a good idea here, but it is not. The problem there is that the atoms may be centered by placing half on the left boundary and half on the right boundary. I find using one logically selected residue or atom is the best method here. 6. Assuming that you got what you wanted in step 5, now run g_traj and g_dist on final_center.gro. In my case, I found that g_traj and g_dist give the same answer as the pull code output when I am using final_center.gro, but not always when I am using final.gro. *** I always laugh when these problems arise because, in an important sense, the protein *did* jump out of the simulation box... at least as far as g_traj and g_dist are concerned. This, we must hope, is correctly treated in the pull code even though it is incorrectly (or at least unintuitively) treated by g_traj and g_dist. Chris. -- original message -- Hi, Thank you Berk and Chris for the suggestions. To address the possibility that this issue is related to periodic boundaries, I used two approaches: 1. The pull group of interest (permeant) was centered in
Re: [gmx-users] g_clustsize
Hi, Use -n without -mol. Clustering will be atom based. Good luck, Ran. Vitaly Chaban wrote: Hi GMX Colleagues, I need a little clarification. I try to calculate a distribution of clusters of ions in a system with several cations and anions and a few solvent molecules. So I just need a number of cluster consisting of ions and the size of the each (how many ions the cluster includes). To do this I use g_clustsize(402) -n index.ndx -mol -s topol.tpr where index.ndx contains only the number of the atoms of the ions. but the programme outputs: Back Off! I just backed up temp.xvg to ./#temp.xvg.1# Reading frame 0 time0.000 Reading file topol.tpr, VERSION 4.0.2 (single precision) Reading file topol.tpr, VERSION 4.0.2 (single precision) Using molecules rather than atoms. Not reading index file index.ndx Why does it not read the index file with the atom number I want to cluster? When I see for example histo-clust.xvg: @title Cluster size distribution @xaxis label Cluster size @yaxis label () @TYPE xy 0 0.000 119.531 2 4.583 3 1.707 4 0.647 5 0.259 6 0.060 7 0.140 8 0.048 9 0.054 10 0.020 11 0.022 12 0.000 57731.096 57833.457 57936.982 58028.942 58131.311 58234.850 58338.401 58430.307 It looks like all the atoms in the system were used to find clusters. And maxclust.xvg: @title Max cluster size @xaxis label Time (ps) @yaxis label #molecules @TYPE xy 0.00e+00 577 1.00e-01 576 2.00e-01 565 3.00e-01 550 4.00e-01 567 5.00e-01 572 6.00e-01 566 7.00e-01 578 8.00e-01 567 9.00e-01 565 1.00e+00 563 1.10e+00 579 1.20e+00 566 Please anybody let me know how to find clusters only among those particles I point out in the index file. So I need only the clusters consisting of ions but solvent is not of interest in my case. Thank you in advance, Vitaly === 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, mob.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- 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: r.fried...@bioc.unizh.ch Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] g_clustsize
Vitaly Chaban wrote: Hi Ran, I will try your advice. And for what purpose should '-mol' be used? To cluster molecules. In this case, you topology is read from the .tpr file and all of the molecules there are taken into account for clustering. Vitaly RF Hi, RF Use -n without -mol. Clustering will be atom based. RF Good luck, RF Ran. RF Vitaly Chaban wrote: Hi GMX Colleagues, I need a little clarification. I try to calculate a distribution of clusters of ions in a system with several cations and anions and a few solvent molecules. So I just need a number of cluster consisting of ions and the size of the each (how many ions the cluster includes). To do this I use g_clustsize(402) -n index.ndx -mol -s topol.tpr where index.ndx contains only the number of the atoms of the ions. but the programme outputs: Back Off! I just backed up temp.xvg to ./#temp.xvg.1# Reading frame 0 time0.000 Reading file topol.tpr, VERSION 4.0.2 (single precision) Reading file topol.tpr, VERSION 4.0.2 (single precision) Using molecules rather than atoms. Not reading index file index.ndx Why does it not read the index file with the atom number I want to cluster? When I see for example histo-clust.xvg: @title Cluster size distribution @xaxis label Cluster size @yaxis label () @TYPE xy 0 0.000 119.531 2 4.583 3 1.707 4 0.647 5 0.259 6 0.060 7 0.140 8 0.048 9 0.054 10 0.020 11 0.022 12 0.000 57731.096 57833.457 57936.982 58028.942 58131.311 58234.850 58338.401 58430.307 It looks like all the atoms in the system were used to find clusters. And maxclust.xvg: @title Max cluster size @xaxis label Time (ps) @yaxis label #molecules @TYPE xy 0.00e+00 577 1.00e-01 576 2.00e-01 565 3.00e-01 550 4.00e-01 567 5.00e-01 572 6.00e-01 566 7.00e-01 578 8.00e-01 567 9.00e-01 565 1.00e+00 563 1.10e+00 579 1.20e+00 566 Please anybody let me know how to find clusters only among those particles I point out in the index file. So I need only the clusters consisting of ions but solvent is not of interest in my case. Thank you in advance, Vitaly === 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, mob.: +38-097-8259698 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Versions of analysis programs
Hi, I've noticed that the VERSION entry of the analysis programs in GMX 4.0.2 is 3.2.0 or 3.3.2, whereas in GMX 3.3.3 it's 3.3.3. Is that just a typo? Thanks, Ran. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] rmsd on homologous protein structure
Hi, For individual structures, you can use g_confrms. If you want a trajectory you can download do_multiprot from the user contributions section, and follow the instructions there. Note that multiprot aligns based on the structure only (no sequence information). Ran. Tatsiana Kirys wrote: Hi, i want to calculate rmsd on homologous protein structures that have different residue numbers. As far as i understood g_rms gives only rmsd of the same structure in different configurations, but it doesn't fit homologous protein structures? In Option -f2 can i provide a trajectory of a homologous protein structure of it also have to be a reserence structure trajectory (which is provided in -s)? many many thanks Tatsiana -- -- 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 -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Peptide aggregation
Dear Leon, Note that you can already use g_clustsize to check the aggregates. I'll contact you off list next week with the modified version. Ran On Fri, 19 Sep 2008 17:13:02 +0100 Léon Salgado [EMAIL PROTECTED] wrote: Dear Dr. Ran Friedman Would you please be so kind to send me your version, to calculate then the rgyr of the largest aggregate. The box was built with a layer of 1.2 nm around the solute (editconf -d 1.2). Leon Ran Friedman wrote: Dear Leon, You can try to use g_clustsize to get the aggregates. I have a version that can calculate the gyration radius of the largest aggregate, but this would work only if your box is big enough and I haven't tried it with rhombic dodecahedron boxes. Ran. Léon Salgado wrote: Dear gmx users I did some simulations of multimers (peptides) in rhombic dodecahedron boxes. In the initial configuration of the system, the peptides are close of each other in the center of the box. My aim to see if the peptides do aggregate during the trajectory or if they tend to stay apart. A rough estimate can be taken from the gyration radius for all the peptides together. Already did a trjconv -pbc nojump pre-treatment on the trajectory, before calculating the Rgyr. The gyration.xvg plots sometimes do show abrupt jumps, and this is surely due to boundary effects, if I correctly understood the PBC idea. If a peptide approaches the boundary, it appears on the opposite side, thus rgyr will show a false sudden increase. In fact, the peptide could be closer to the rest of the other peptide molecule(s). Thus my question is: how to deal with peptide clusters that span over the periodic boundaries? A similar question was done by Singh: http://www.gromacs.org/pipermail/gmx-users/2007-January/025474.html and it was suggested by Chris Neale to pre-process the trajectory (see http://www.gromacs.org/pipermail/gmx-users/2007-January/025481.html) with: trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump but I'm getting infinite loops on the -pbc cluster treatment, same as reported by Chris (http://www.gromacs.org/pipermail/gmx-users/2008-July/035343.html). Best, Léon ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6355593 Skype: ran.friedman -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Peptide aggregation
Dear Leon, You can try to use g_clustsize to get the aggregates. I have a version that can calculate the gyration radius of the largest aggregate, but this would work only if your box is big enough and I haven't tried it with rhombic dodecahedron boxes. Ran. Léon Salgado wrote: Dear gmx users I did some simulations of multimers (peptides) in rhombic dodecahedron boxes. In the initial configuration of the system, the peptides are close of each other in the center of the box. My aim to see if the peptides do aggregate during the trajectory or if they tend to stay apart. A rough estimate can be taken from the gyration radius for all the peptides together. Already did a trjconv -pbc nojump pre-treatment on the trajectory, before calculating the Rgyr. The gyration.xvg plots sometimes do show abrupt jumps, and this is surely due to boundary effects, if I correctly understood the PBC idea. If a peptide approaches the boundary, it appears on the opposite side, thus rgyr will show a false sudden increase. In fact, the peptide could be closer to the rest of the other peptide molecule(s). Thus my question is: how to deal with peptide clusters that span over the periodic boundaries? A similar question was done by Singh: http://www.gromacs.org/pipermail/gmx-users/2007-January/025474.html and it was suggested by Chris Neale to pre-process the trajectory (see http://www.gromacs.org/pipermail/gmx-users/2007-January/025481.html) with: trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump but I'm getting infinite loops on the -pbc cluster treatment, same as reported by Chris (http://www.gromacs.org/pipermail/gmx-users/2008-July/035343.html). Best, Léon ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- -- 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 -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] About QH entropy, could you please help me?
Dear Li Yang, I forward your email to the GMX mailing list, which may be better for you since other users can contribute as well. I'll reply there - I hope you've subscribed to the list. Ran. Li Yang wrote: Dear Ran Friedman I'm sorry to disturb you, my name is Li Yang, I'm a chinese student. I've read some paper about the calculation of QH entropy: (a)Jurgen Schlitter_ChemPhysLett1993_215_617, (b)Ioan Andricioaei_JChemPhys2001_115_6289(quasiharmonic approximation). There is still something confuse me. (1) Why the number of the eigenvalues is 3n-6 (the last 6 values are close to zero) but not 3n ? I practice some small examples by gromacs. (256 argon atoms in a box of 2.3nm^3, you can find this example in paper(b)). For g_covar, when -nofit, the number of eigenvalues is 3n; when -fit the number is 3n-6. It seems there are some freedoms constrainted in the fit process. The paper' conclusion is based on a assumption that hwkT, say, the high frequencies vibrate (both rotation and translations, right?) can be omitted for the entropy calculations, as it were, the contributions of them is too small to be omitted. Are the freedoms mentioned above represent the freedoms of rotations and translations of the molecules. I don't know. Maybe the answer is in those papers, but I cannot catch it. While how to use the nofit result and fit result? The eigenv.agr in the attachment includes fit and nofit results for the example: 256 argon atoms in a box of 2.3nm^3. Why there is a big difference between them? (2) I split some time-segment to obtain the entropies in each stage to get the convergence variation of the entropy. But I doubt the feasibility of this method. If wrong, how to do? eg, time points: 0, 1, 2, 3, 4, 5. and time stage：0-1, 0-2, 0-3, 0-4, 0-5, right? why not 0-1, 1-2, 2-3, 3-4, 4-5. In the maillist of gmx, the latter is not wrong because of undersampling, I don't know this meaning. Could you please offer me some suggestions or refs? (3) In entropy calculations, a system need to run a long time for entropy convergence, the time seems to be longer than the one which needed for energy convergence. While, for equilibrium thermodynamics simulations, how to justify whether or not the system has achieving a equilibrium stage, based on energy convergence or entropy confvergence? (4) For the example mentioned in the paper Ioan Andricioaei_JChemPhys2001_115_6289. I use your perl script for entropy calculation. But I don't reproduce the result. The needed time of entropy convergence is longer than the time mentioned in the paper, and so larger of my entropy. I don't know why, perphas the simulation conditions is not right. My simulation files are included in the attachment. Could you give some suggestions? BTW, in line 77 of your script: $w=$ev*$u*10**(-18), Does 10^-18 mean nm^-2? I apologize in advance if I disturb you. Thank you very much. Waiting for you reply. Best Li Yang Li Yang [EMAIL PROTECTED] 2008-09-17 -- -- 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 -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] About QH entropy, could you please help me?
(1) 6 eigenvalues represent rotation and translation. For (very) small molecules, these can be quite substantial, see Carlsson and Aqvist, /J. Phys. Chem. B,/ *109* (13), 6448 -6456, 2005. By fitting you remove the rotation and translation. You can search the literature for papers that discuss the QH approximation as well. The motions are not really harmonic - this is why it's an approximation. I've received very similar results to Carlsson and Aqvist for benzene and palmatic acid with GMX. (2) The values you get depend on the sampling and the conversion of the simulations. To improve sampling, you have to store the coordinates frequently enough (so you get more samples). In addition, the simulation should be long enough to give you meaningful results - and both depend on the system which you study. Checking for convergence can be done by repeating the calculations on different time windows, as you suggested. (3) If you want to study the entropy, you have to sure it convergence. Otherwise, it depends on what you want to calculate. (4) Try to see if you really simulate the same system, and maybe try other systems like the ones in the above mentioned paper. There can be dozens of things that can change and since I didn't run these simulations I can't be of much help here. As for the units, I don't really remember what I used for frequencies, only that the final result should be in J/(mol K) or Cal/(mol K). By following the script, with the remarks, you should get the right units. Ran. Ran Friedman wrote: Dear Li Yang, I forward your email to the GMX mailing list, which may be better for you since other users can contribute as well. I'll reply there - I hope you've subscribed to the list. Ran. Li Yang wrote: Dear Ran Friedman I'm sorry to disturb you, my name is Li Yang, I'm a chinese student. I've read some paper about the calculation of QH entropy: (a)Jurgen Schlitter_ChemPhysLett1993_215_617, (b)Ioan Andricioaei_JChemPhys2001_115_6289(quasiharmonic approximation). There is still something confuse me. (1) Why the number of the eigenvalues is 3n-6 (the last 6 values are close to zero) but not 3n ? I practice some small examples by gromacs. (256 argon atoms in a box of 2.3nm^3, you can find this example in paper(b)). For g_covar, when -nofit, the number of eigenvalues is 3n; when -fit the number is 3n-6. It seems there are some freedoms constrainted in the fit process. The paper' conclusion is based on a assumption that hwkT, say, the high frequencies vibrate (both rotation and translations, right?) can be omitted for the entropy calculations, as it were, the contributions of them is too small to be omitted. Are the freedoms mentioned above represent the freedoms of rotations and translations of the molecules. I don't know. Maybe the answer is in those papers, but I cannot catch it. While how to use the nofit result and fit result? The eigenv.agr in the attachment includes fit and nofit results for the example: 256 argon atoms in a box of 2.3nm^3. Why there is a big difference between them? (2) I split some time-segment to obtain the entropies in each stage to get the convergence variation of the entropy. But I doubt the feasibility of this method. If wrong, how to do? eg, time points: 0, 1, 2, 3, 4, 5. and time stage：0-1, 0-2, 0-3, 0-4, 0-5, right? why not 0-1, 1-2, 2-3, 3-4, 4-5. In the maillist of gmx, the latter is not wrong because of undersampling, I don't know this meaning. Could you please offer me some suggestions or refs? (3) In entropy calculations, a system need to run a long time for entropy convergence, the time seems to be longer than the one which needed for energy convergence. While, for equilibrium thermodynamics simulations, how to justify whether or not the system has achieving a equilibrium stage, based on energy convergence or entropy confvergence? (4) For the example mentioned in the paper Ioan Andricioaei_JChemPhys2001_115_6289. I use your perl script for entropy calculation. But I don't reproduce the result. The needed time of entropy convergence is longer than the time mentioned in the paper, and so larger of my entropy. I don't know why, perphas the simulation conditions is not right. My simulation files are included in the attachment. Could you give some suggestions? BTW, in line 77 of your script: $w=$ev*$u*10**(-18), Does 10^-18 mean nm^-2? I apologize in advance if I disturb you. Thank you very much. Waiting for you reply. Best Li Yang Li Yang [EMAIL PROTECTED] 2008-09-17 -- -- 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
