Re: [gmx-users] Re: Re: FEP problem with lambda perturbation 1 to 0.95
So what you mean is that I should either use soft core for the entire transformation or not use it at all. But then I do not understand what Carsten said about using at least on lambda values close to 0 and 1. I thought that if I used soft core on the last point of my transformation (the one that crashed before I used soft core) I would eliminate the singularities produced by the end points. I got a little confused now. right, I see the confusion now - I don't agree with the way Carsten's phrased that, for a single free energy calculation you absolutely have to use a single consistent set of parameters. At end points lambda=0 and 1, the soft core potential is identical to standard vdW / electrostatics; this means the free energy difference for switching on a soft core potential at either end point is zero. When lambda is not =0 or =1, this is no longer true, so if you activate the soft core potential part way through there would be a free energy difference which isn't being counted. hope that helps, Floris Hi Fabricio, It's not correct to change your value of alpha, you should use a single value for the whole transformation. The soft core potential is constructed so that the end points at lambda=0 and 1 represent the 'native' states (with no influence from the soft core parameters), and that intermediate values produce a smooth transformation. Best, Floris From: Ragnarok sdf fabrac...@gmail.com To: gmx-users@gromacs.org Sent: Monday, 10 August, 2009 20:54:35 Subject: [gmx-users] Re: Re: FEP problem with lambda perturbation 1 to 0.95 I have tried using the soft core correction for values of lambda above 0.5, because i read that the overlaping starts usually at this lambda value. The problem is that now I values of deltaG where lambda is near 0.5 a little bit off-scale. What I mean is that what used to be a nice sequencial decrease in values from lambda 0 to lambda 1, now gives me a crazy value for lambda 0.5 (by crazy I mean 3 times larger) then for lambda 0.55, 0.6, 0.65 etc, I get values 3 times smaller than what they used to be. I guess that maybe using soft core correction for lambda values starting from 0.5 was a little bit to soon. But then for which lambda values should I start using soft core and how would I justify my choice? Thank you Fabrэcio Bracht - Ocultar texto das mensagens anteriores - I agree with Carsten. See perhaps the discussion at www.alchemistry.org as well. On Fri, Aug 7, 2009 at 2:35 AM, Carsten Kutzner ckut...@gwdg.de wrote: On Aug 6, 2009, at 10:57 PM, Ragnarok sdf wrote: I am performing FEP do obtain the dimerization of a protein in membrane. The lambda intervals i am using are 0.05 for each window. After that I rerun each lambda .trr perturbing the system (plus)0.05 and (minus)0.05 lambda value. Then with g-energy I obtain the deltaG for each delta lambda. Well, I have encountered a problem when trying to simulate the last window (1.0 - 0.95 ). The simulation runs for a while and then dies. The log file says Step 2200 Warning: Pressure scaling more than 1%. Hi Fabricio, do you use soft-core? If not, I think you need to, at least for the intervals next to 0 and 1 to avoid singularities (these can result in undefined / NaN forces). See chap. 4.5.1 and 7.3.23 in the manual. Carsten ___ 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] energy minimization
Hi, On Wed, Aug 12, 2009 at 3:06 AM, Mark Abrahammark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Dear all, I performed an md simulation but it crashed at the beginning because according to it system was exploding. Also when I tried to see the system by ngmx, there was no water anymore and it was only the molecule sitting in the box(after grompp and before mdrun it was a box of water plus the molecule)!!?? So you used a wrong file at some point... name your files carefully, and use them carefully. Maybe xtc-grps was set to protein? That wouldn't be related to the problem. But did the crash occur directly, at step -1/0/1, or did the system run at least for a few steps? What exactly were you doing? Please copy-paste your command lines, your .mdp file and the mdrun output (not the log file yet, please). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] Improper Dihedrals
Hi, If you turn all bonds to constraints, and your system is infinitely periodic, you probably don't even need impropers. The bond lengths can only be satisfied in the plane. Adding impropers, straining your molecule further into the configuration you think is proper, adds forces that inevitable come with vibrations. The higher the straining (the forces), the higher the frequencies, the smaller you have to set your time step to be sure not to get into trouble. Then again, everything moves and surely graphene sheets vibrate. The big question here is: what is the out of plane vibration of atoms in a graphene sheet? Googling graphene out plane vibration gives the following for a first hit: http://www.iop.org/EJ/article/0370-1301/69/12/319/prbv69i12p1326.pdf Maybe that's a good start to get your system tuned? Cheers, Tsjerk On Tue, Aug 11, 2009 at 9:41 PM, Justin A. Lemkuljalem...@vt.edu wrote: Darrell Koskinen wrote: Dear GROMACS Gurus, I assigned improper dihedrals to my graphene structuure but still see it vibrating. Is this to be expected? I thought the purpose of improper dihedrals was to keep planar structures planar. There is still a force constant associated with the improper, so deviations from absolute planarity are possible. Vibrations aren't unexpected, but any severe distortions would be problematic. -Justin Here is a copy of a couple of sections of my topology file after assigning the improper dihedrals to my graphene structure: #define improper_dihedral improper_Z_CA_X_Y [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 3 1 2 5 1 improper_dihedral 2 1 3 7 1 improper_dihedral 2 1 4 9 1 improper_dihedral 1 2 5 11 1 improper_dihedral 1 2 6 13 1 improper_dihedral ___ gmx-users mailing list gmx-us...@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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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-us...@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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] copper cluster bond to histidines
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
--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
http://sites.google.com/site/andreaspitaleri/
---
-
La tua mano puo' lasciare un segno importante.
Dona il tuo 5 per mille al San Raffaele di Milano.
E' SEMPLICE E NON COSTA NULLA.
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Finanziamento della ricerca sanitaria
il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
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Re: [gmx-users] copper cluster bond to histidines
Hi Andrea,
You're probably best off 'fixing' the copper to the protein, meaning
introducing bonds at least (harmonic, type 6?). With these bonds you
can to some degree account for the effects of polarization and such on
the interatomic distances, which are likely more difficult to model
reparameterizing the non-bonded interactions. You should also
definitely consider that there is considerable polarization and charge
transfer in such metal clusters, which means that you should probably
attenuate the charges of the copper as well as of the ligating atoms.
For the ligation geometry you can try to rely on size-exclusion
effects of the ligands, but copper may prove nasty, in which case you
also need to set parameters for angles and maybe for dihedrals. Not
for naught that newbies are usually discouraged for performing
simulations like these (exotic species)... But you had already
considered that.
Hope this helps,
Tsjerk
On Wed, Aug 12, 2009 at 12:40 PM, andrea
spitalerispitaleri.and...@hsr.it 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
--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
http://sites.google.com/site/andreaspitaleri/
---
-
La tua mano puo' lasciare un segno importante.
Dona il tuo 5 per mille al San Raffaele di Milano.
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei redditi
Finanziamento della ricerca sanitaria
il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Per saperne di piu': 5permi...@hsr.it o vai sul sito http://www.5xmille.org.
___
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Please search the archive at http://www.gromacs.org/search before posting!
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
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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] copper cluster bond to histidines
Hi Tsjerk,
thanks for the usual useful suggestions! Probably I will go for that, add an
harmonic bonds between
Cu2+ and N-HIS and I will think how to hand the charges too.
Probably this is the less worst solution for now.
Thank a lot,
Regards
andrea
Tsjerk Wassenaar wrote:
Hi Andrea,
You're probably best off 'fixing' the copper to the protein, meaning
introducing bonds at least (harmonic, type 6?). With these bonds you
can to some degree account for the effects of polarization and such on
the interatomic distances, which are likely more difficult to model
reparameterizing the non-bonded interactions. You should also
definitely consider that there is considerable polarization and charge
transfer in such metal clusters, which means that you should probably
attenuate the charges of the copper as well as of the ligating atoms.
For the ligation geometry you can try to rely on size-exclusion
effects of the ligands, but copper may prove nasty, in which case you
also need to set parameters for angles and maybe for dihedrals. Not
for naught that newbies are usually discouraged for performing
simulations like these (exotic species)... But you had already
considered that.
Hope this helps,
Tsjerk
On Wed, Aug 12, 2009 at 12:40 PM, andrea
spitalerispitaleri.and...@hsr.it 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
--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
http://sites.google.com/site/andreaspitaleri/
---
-
La tua mano puo' lasciare un segno importante.
Dona il tuo 5 per mille al San Raffaele di Milano.
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei redditi
Finanziamento della ricerca sanitaria
il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Per saperne di piu': 5permi...@hsr.it o vai sul sito
http://www.5xmille.org.
___
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
--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
http://sites.google.com/site/andreaspitaleri/
---
-
La tua mano puo' lasciare un segno importante.
Dona il tuo 5 per mille al San Raffaele di Milano.
E' SEMPLICE E NON COSTA NULLA.
Basta indicare nell'apposito riquadro della dichiarazione dei redditi
Finanziamento della ricerca sanitaria
il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor:
03 06 42 80 153 e ricordarsi di firmare.
Per saperne di piu': 5permi...@hsr.it o vai sul sito http://www.5xmille.org.
___
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] energy minimization
Dear all, Thanks for all comments. I will check again all steps for my previous simulation with right files (according to Mark) and then I will let you know if I got the same problem (I am not working on proteins). Another question: --After energy minimization step for in-vacuo run, Should I do still position restrained MD, since I want the bond length be fixed (constraints=all-bonds)? --After pr-md in mdrun step for in-vacuo simulation, is it true that I will get the movement of my molecule in vacuum?? I appreciate your help/Jamie On Wed, Aug 12, 2009 at 3:53 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi, On Wed, Aug 12, 2009 at 3:06 AM, Mark Abrahammark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Dear all, I performed an md simulation but it crashed at the beginning because according to it system was exploding. Also when I tried to see the system by ngmx, there was no water anymore and it was only the molecule sitting in the box(after grompp and before mdrun it was a box of water plus the molecule)!!?? So you used a wrong file at some point... name your files carefully, and use them carefully. Maybe xtc-grps was set to protein? That wouldn't be related to the problem. But did the crash occur directly, at step -1/0/1, or did the system run at least for a few steps? What exactly were you doing? Please copy-paste your command lines, your .mdp file and the mdrun output (not the log file yet, please). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] minimization
Dear users I have a dimer protein which I want to minimized it..unfortunately the protein is in high energy level and before starting to minimize it explode. I already went through users email and also wiki gromacs and also I tried all the way like changing time step, change coulomb type ,... but they did not work .. As MARK suggest me I try to minimize monomer separately but the monomers itself also have high energy and it is not possible to minimize them... I change the forcefield from olps to gromacs and minimization work. I did several minimization by gromacs forcefiled and then I tried to minimized the system by OPLS but again the system start exploiding... Is there any idea that why the minimization work by gromacs but not work with opls? finally I should simulate my system by opls and if I want to do it my system still not minimized for OPLS I will apprecite if there will be some idea for my problem 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] energy minimization
Jamie Seyed wrote: Dear all, Thanks for all comments. I will check again all steps for my previous simulation with right files (according to Mark) and then I will let you know if I got the same problem (I am not working on proteins). Another question: --After energy minimization step for in-vacuo run, Should I do still position restrained MD, since I want the bond length be fixed (constraints=all-bonds)? --After pr-md in mdrun step for in-vacuo simulation, is it true that I will get the movement of my molecule in vacuum?? I appreciate your Position restraints are most commonly used to allow solvent to relax around a structure during initial equilibration. If you're running in vacuo, I don't see much purpose. It is possible that your molecule will still move; PR does not mean that you are fixing atoms in place, but instead that you are specifying an energy penalty for moving the constituent atoms away from their original coordinates. -Justin help/Jamie On Wed, Aug 12, 2009 at 3:53 AM, Tsjerk Wassenaar tsje...@gmail.com mailto:tsje...@gmail.com wrote: Hi, On Wed, Aug 12, 2009 at 3:06 AM, Mark Abrahammark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: Jamie Seyed wrote: Dear all, I performed an md simulation but it crashed at the beginning because according to it system was exploding. Also when I tried to see the system by ngmx, there was no water anymore and it was only the molecule sitting in the box(after grompp and before mdrun it was a box of water plus the molecule)!!?? So you used a wrong file at some point... name your files carefully, and use them carefully. Maybe xtc-grps was set to protein? That wouldn't be related to the problem. But did the crash occur directly, at step -1/0/1, or did the system run at least for a few steps? What exactly were you doing? Please copy-paste your command lines, your .mdp file and the mdrun output (not the log file yet, please). Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org mailto: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 mailto: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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] Re: [gmx-developers] Fwd: xdrfile library, read co-ordinates from .xtc
Janne, Jussi, Thank you very much! Vitaly On Wed, Aug 12, 2009 at 11:35 AM, Janne Blomqvistjanne.blomqv...@tkk.fi wrote: Vitaly V. Chaban wrote: On the same topic, I have a question to the community: does anybody try to make *so*-library (or *dll* on windows) of xdrfile in order to use with other programming languages? I spent a day trying to master this art but didn't still succeed. If somebody more experienced with dynamic libraries than me can provide such one, I will be very grateful. Yeah, I did this on Linux, in order to call libxdrfile using the python ctypes library. I just configured xdrfile with --enable-shared. -- Janne Blomqvist ___ 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] A question regarding single sum virial
Hello all, I got a question when I read the the manual chapter for the single sum virial (p195-196). In eq (B.3) we have r_ij_n=r_i+delta_i-r_j. Shouldn't delta here also depend on index j? I think delta is zero when particle i and j are close. And delta can be something else when any x/y/z component of r_i-r_j is larger than half box length. But from eq (B.5) to (B.11) it seems delta_i only depends on index i and I got confused. Could anyone explain it to me? Thanks very much! Lanyuan Lu _ Messenger安全保护中心，免费修复系统漏洞，保护Messenger安全！ http://im.live.cn/safe/___ 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] A question regarding single sum virial
Hi Lanyuan Lu, It's described in detail in Chapter 2 of Henk Bekkers PhD thesis, available at: http://dissertations.ub.rug.nl/faculties/science/1996/h.bekker/ Cheers, Tsjerk 2009/8/12 LuLanyuan lulany...@msn.com: Hello all, I got a question when I read the the manual chapter for the single sum virial (p195-196). In eq (B.3) we have r_ij_n=r_i+delta_i-r_j. Shouldn't delta here also depend on index j? I think delta is zero when particle i and j are close. And delta can be something else when any x/y/z component of r_i-r_j is larger than half box length. But from eq (B.5) to (B.11) it seems delta_i only depends on index i and I got confused. Could anyone explain it to me? Thanks very much! Lanyuan Lu 使用新一代 Windows Live Messenger 轻松交流和共享！ 立刻下载！ ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] problem installing gromacs
Hi There, I have some problems installing gromacs on the linux server. fftw installed with no error, but when I install gromacs, I got the following error: * /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/home/y1gao/soft/fftw/lib -o grompp grompp.o libgmxpreprocess_d.la ../mdlib/l cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o .libs/grompp grompp.o -L/home/y1gao/soft/fftw/lib ./.libs/libgmxpreprocess_d.a -L/usr/X11R6/lib ../mdlib/.libs/libmd_d.so /n _d.so -lnsl -lfftw3 -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/home/y1gao/soft/gromacs//lib ../mdlib/.libs/libmd_d.so: undefined reference to `__libm_sse2_sincos' ../mdlib/.libs/libmd_d.so: undefined reference to `__libm_sse2_log' ../mdlib/.libs/libmd_d.so: undefined reference to `_intel_fast_memcpy' collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src' make: *** [all-recursive] Error 1 *** I used the combinations of the following fftw and gromacs: fftw 3.2.1; fftw3.2.2 gromacs 3.3.3; gromacs 4.0.4 gcc version 3.4.6 The command I used are: * To install fftw: $ ./configure --enable-threads --enable-sse2 -prefix /home/y1gao/soft/fftw/lib $ make $ make install To install gromacs: $ ./configure --enable-shared LDFLAGS='-L/home/y1gao/soft/fftw/lib' CPPFLAGS='-I/home/y1gao/soft/fftw/include' --enable-double --prefix=/home/y1gao/soft/gromacs/ $ make $ make install ( error comes out here) * Could anyone help me find a way out? Thanks in advance. Stone ___ 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] A question regarding single sum virial
That's cool. Thanks a lot! Lanyuan Date: Wed, 12 Aug 2009 22:01:14 +0200 Subject: Re: [gmx-users] A question regarding single sum virial From: tsje...@gmail.com To: gmx-users@gromacs.org Hi Lanyuan Lu, It's described in detail in Chapter 2 of Henk Bekkers PhD thesis, available at: http://dissertations.ub.rug.nl/faculties/science/1996/h.bekker/ Cheers, Tsjerk 2009/8/12 LuLanyuan lulany...@msn.com: Hello all, I got a question when I read the the manual chapter for the single sum virial (p195-196). In eq (B.3) we have r_ij_n=r_i+delta_i-r_j. Shouldn't delta here also depend on index j? I think delta is zero when particle i and j are close. And delta can be something else when any x/y/z component of r_i-r_j is larger than half box length. But from eq (B.5) to (B.11) it seems delta_i only depends on index i and I got confused. Could anyone explain it to me? Thanks very much! Lanyuan Lu 使用新一代 Windows Live Messenger 轻松交流和共享！ 立刻下载！ ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 _ 张三挖到了元宝,小美又掉进陷阱了,快来MClub与好友齐乐乐！立刻访问！ http://club.msn.cn/?from=3___ 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] A question regarding single sum virial
Hello, Unfortunately I still don't understand the equations in the manual after reading Chapter 2 of Hendrik Bekker's dissertation. In that chapter, the virial is expressed as A+B+C. Here A+B is the r_i*F_i stuff, which can be considered as the virial without considering PBC. And the third term should correspond to the detla derm in the Gromacs manual, which is a correction due to PBC. However, in the dissertation the correction term is always related to pairwise forces F_ij in different ways to calculate it. In the manual, the correction term is written as delta_i*F_i, which is related to individual force on each atom only. I still have no idea for that how the magic delta can convert a pairwise force expression into an individual force expression. Anyone has an idea about it? Thanks, Lanyuan Date: Wed, 12 Aug 2009 22:01:14 +0200 Subject: Re: [gmx-users] A question regarding single sum virial From: tsje...@gmail.com To: gmx-users@gromacs.org Hi Lanyuan Lu, It's described in detail in Chapter 2 of Henk Bekkers PhD thesis, available at: http://dissertations.ub.rug.nl/faculties/science/1996/h.bekker/ Cheers, Tsjerk 2009/8/12 LuLanyuan lulany...@msn.com: Hello all, I got a question when I read the the manual chapter for the single sum virial (p195-196). In eq (B.3) we have r_ij_n=r_i+delta_i-r_j. Shouldn't delta here also depend on index j? I think delta is zero when particle i and j are close. And delta can be something else when any x/y/z component of r_i-r_j is larger than half box length. But from eq (B.5) to (B.11) it seems delta_i only depends on index i and I got confused. Could anyone explain it to me? Thanks very much! Lanyuan Lu 使用新一代 Windows Live Messenger 轻松交流和共享！ 立刻下载！ ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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 _ 您可以借助 Windows Live 整理、编辑和共享您的照片。 http://www.microsoft.com/china/windows/windowslive/products/photo-gallery-edit.aspx___ 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] use Xcode to debug Gromacs
Dear all, -- Shuangxing Dai ___ 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] use Xcode to debug Gromacs
Dear all, I was trying to use Xcode to debug the file mdrun and hope to trace the flow of source file by running a simple case. There is a tutorial for using Xcode to debug a package named apbs, which is very like Gromacs, here: http://www.macresearch.org/tutorial-introducing-xcode-30-organizer I followed the tutorial and it works well for apbs. But when I did the same thing for Gromacs, I can only see the assemble code for mdrun and it was not connected to the source code. Only assemble code does not help. So my question is: anyone know how to use Xcode to debug Gromacs executable file? I need the breakpoints to be related with the source code so that I can trace the flow. Sorry for the last mail that I pressed space accidently... Thank you in advance. -- Shuangxing Dai ___ 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] Determining the energy of an individual atom
Hi Mark, I do have a paper in my possession that provides a first principles calculation of the adsorption energy of ammonia on graphene. I was planning on using this paper to compare the adsorption energy to the vibrational energy of the individual atoms in the graphene lattice. But how do I measure the average kinetic energy of a graphene atom in my system? And I should also let you know that I have removed the ad hoc parameters and am using ffoplsaa in its pure unmodified form. Thanks again for your help. Darrell Date: Wed, 12 Aug 2009 13:42:08 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Determining the energy of an individual atom. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a823a10.6010...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Dear GROMACS Gurus, In my simulation of a graphene structure surrounded by an ammonia gas, I am not seeing any adsorption of the ammonia molecules onto the surface of the graphene structure. I am wondering if the reason I am not seeing any absorption is because the graphene lattice is vibrating and thereby imparting too much energy to the ammonia molecule when it comes into the vicinity of the graphene lattice, thus impairing any adsorption. I assume that the adsorption energy would have to be significantly greater than the vibrational energy in order to allow adsorption to occur. If this is true, then is there some way of determining the translational (vibrational) energy of an atom in the graphene lattice so that I may compare it to the adsorption energy? You can measure the average kinetic energy of an atom, but whether you can infer anything else might depend on comparing with a structure to which something did adsorb. Frankly, it seems rather more likely that the ad hoc combination of parameters you have described in the past is incapable of modelling this behaviour. Parameterization is only known to be useful within a limited domain. You might be able to demonstrate transferability, but it cannot be assumed. 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
[gmx-users] Determining the energy of an individual atom
Hi David, Thank you for your comments. The bulk of the graphene sheet is not polarized in the absence of a connection to electrodes. In some experiments on graphene adsorption, they show significant adsorption of ammonia, but in these experiments they connected the graphene sheet to electrodes. Could this be assisting in the adsorption of ammonia on the graphene sheet? The edges of my graphene sheet are polarized since I have terminated the edges with hydrogen atoms. I expected to see some adsorption in the bulk of the graphene sheet resulting from VdW forces and significantly more adorption on the edges due to the polarization. I also expected to see a stronger adsorption energy for the adsorption on the edges. However, I am not seeing even a single molecule being adsorbed either in the bulk or on the edges. Could it be that the binding energy arising from VdW forces is much weaker than the vibrational energy of the lattice atoms? I should also add that hydrogen atoms attached to the edge of the graphene lattice show even greater movement than the carbon atoms in the graphene lattice. Is this is to be expected and is it the result of the small mass of the hydrogen atoms and could this be impairing the adsorption on the edges? Again, your thoughts and comments are much appreciated. Darrell Date: Wed, 12 Aug 2009 07:45:11 +0200 From: David van der Spoel sp...@xray.bmc.uu.se Subject: Re: [gmx-users] Determining the energy of an individual atom. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a8256e7.2030...@xray.bmc.uu.se Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Dear GROMACS Gurus, In my simulation of a graphene structure surrounded by an ammonia gas, I am not seeing any adsorption of the ammonia molecules onto the surface of the graphene structure. I am wondering if the reason I am not seeing any absorption is because the graphene lattice is vibrating and thereby imparting too much energy to the ammonia molecule when it comes into the vicinity of the graphene lattice, thus impairing any adsorption. I assume that the adsorption energy would have to be significantly greater than the vibrational energy in order to allow adsorption to occur. If this is true, then is there some way of determining the translational (vibrational) energy of an atom in the graphene lattice so that I may compare it to the adsorption energy? If your graphene is not polarizable then the interaction with ammonia is limited to Van der waals interactions. However the induced polarization can be quite strong for such groups, and hence it seems you are missing an important part of the binding energy. Thanks again for your help. Darrell ___ 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] bad bond in polymer
Hi gmx-users, I am building a polymer and I've added the monomer unit to the .rtp file. The final structure appears with an undesired bond between the monomer units at the extremes of the polymer. How can I prevent the monomers at the end forming the bond? I have read other post like http://www.mail-archive.com/gmx-users@gromacs.org/msg21133.html but can not avoid this problem . Thank you in advance veduardo. Lab. de Fisicoquímica Molecular Facultas de Ciencias Universidad de Chile ___ 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] bad bond in polymer
nicegromacs wrote: Hi gmx-users, I am building a polymer and I've added the monomer unit to the .rtp file. The final structure appears with an undesired bond between the monomer units at the extremes of the polymer. How can I prevent the monomers at the end forming the bond? Bonds that appear in visualization software are separate from bonds that exist in the topology. Programs like VMD guess where bonds should be based on atomic distances, which may or may not correspond to reality. Be assured that the only true bonds are the ones you have defined in the topology. -Justin I have read other post like http://www.mail-archive.com/gmx-users@gromacs.org/msg21133.html but can not avoid this problem . Thank you in advance veduardo. Lab. de Fisicoquímica Molecular Facultas de Ciencias Universidad de Chile ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] Fatal Equilibration Errors
Hello, In an earlier message, it was stated that topolbuild generated topologies with Gromos 53a6 and OPLS-AA force fields. I am using topolbuild (version 1.2.2), and the only files in the dat/gromacs directory are for the force fields: 43a1, 43a2, 43b1, 45a3, 53a5, and 53a6. How is the OPLS-AA force field used? Thank you. Nancy On Mon, Aug 10, 2009 at 6:22 PM, Bruce D. Ray bruced...@yahoo.com wrote: On Sunday, August 9, 2009 at 4:32:19 PM, Nancy nancy5vi...@gmail.com wrote: I obtained the ethylene glycol (1,2-ethanediol) structure from the URL: http://www.rcsb.org/pdb/files/ligand/EDO_ideal.pdb I converted the EDO_ideal.pdb file into ethanediol.mol2 using UCSF Chimera (http://www.cgl.ucsf.edu/chimera/). I then use topolbuild 1.2 (written by Dr. Bruce D. Ray) to generate the topologies: $ .../topolbuild1_2_2/src/topolbuild -n ethanediol -dir .../topolbuild1_2_2/dat/gromacs -ff gmx53a6 which outputs the files: ethanediol.gro ethanediol.log ethanediolMOL.mol2 ethanediol.top ffethanediol.itp posreethanediol.itp I modified the ffethanediol.itp file to read: === #define _FF_GROMOS96 #define _FF_GROMOS53A6 #define _FF_USER [ defaults ] ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 1 no 1.0 1.0 #include ffG53a6nb.itp === The lack of hydrogen bonds between the solute and solvent molecules was due to the lack of charges in the generated topology file ethanediol.top. So I changed the atoms section of the topology file (the original topology file is at the end of this message), and this causes hydrogen bonds between the solute and solvent in numbers comparable to that between the solvent molecules. === [ atoms ] ; nrtype resnr residu atom cgnrcharge mass 1 CH2 1 EDO C11 0.17600 14.02700 ; 0.000 2OA 1 EDO O11 -0.5740 15.99940 ; 0.000 3H 1 EDO HO11 0.39800 1.00800 ; 0.000 4 CH2 1 EDO C22 0.17600 14.02700 ; 0.000 5OA 1 EDO O22 -0.5740 15.99940 ; 0.000 6H 1 EDO HO22 0.39800 1.00800 ; 0.000 ; total molecule charge = 0.000 === I obtained the charge values from the methanol tutoral included with Gromacs (.../share/gromacs/tutor/methanol/methanol.itp). I then enlarge the box and solvate the molecule: I used a mol2 file that I generated from a sy2 file downloaded from NCI by first running the file through dos2unix then replacing the 0 in the residue number column with 1 EDO so that I had both a correct residue number column with a residue name column. The NCI data was missing the residue name column. I then read the mol2 file that resulted into UCSF Chimera and used it to generate gasteiger charges for ethylene glycol. Chimera wrote the following mol2 file as a result: @TRIPOSMOLECULE EDO 10 9 1 0 0 SMALL AMBER99 @TRIPOSATOM 1 O1 0.0.0. O.3 1 EDO -0.3940 2 C1 -0.9400 -0.1600 -1.0400 C.3 1 EDO 0.0662 3 C2 -1.74001.1400 -1.1400 C.3 1 EDO 0.0662 4 O2 -2.52001.28000.0200 O.3 1 EDO -0.3940 5 H1 0.5196 -0.80240.0879 H 1 EDO 0.2102 6 H2 -1.5882 -0.9871 -0.8384 H 1 EDO 0.0588 7 H3 -0.4343 -0.3499 -1.9636 H 1 EDO 0.0588 8 H4 -2.37211.1133 -2.0029 H 1 EDO 0.0588 9 H5 -1.06961.9696 -1.2252 H 1 EDO 0.0588 10 H6 -3.02712.0935 -0.0316 H 1 EDO 0.2102 @TRIPOSBOND 115 1 212 1 327 1 426 1 523 1 639 1 738 1 834 1 94 10 1 @TRIPOSSUBSTRUCTURE 1 EDO 2 RESIDUE 4 A EDO 0 ROOT I processed this with topolbuild 1.3 and generated topologies with gromacs 53a6 and with opls-aa as the force fields. I am attaching the results to this as the tarred and gzipped file, ethanediol.tgz I note that the opls-aa atom types selected by topolbuld 1.3 have characteristic atom type charges charges of -0.7 for each oxygen, +0.435 for each of the two hydrogens bound to oxygens, +0.06 for each of the hydrogens bound to carbon, and +0.145 for each of the carbons. The comparison to the gasteiger charges Chimera assigned to these atoms is interesting. The opls-aa topology generated also assigns to the O1-C1-C2-O2 dihedral the diol constants found as a special define in
Re: [gmx-users] use Xcode to debug Gromacs
Shuangxing Dai wrote: Dear all, I was trying to use Xcode to debug the file mdrun and hope to trace the flow of source file by running a simple case. There is a tutorial for using Xcode to debug a package named apbs, which is very like Gromacs, here: http://www.macresearch.org/tutorial-introducing-xcode-30-organizer I followed the tutorial and it works well for apbs. But when I did the same thing for Gromacs, I can only see the assemble code for mdrun and it was not connected to the source code. Only assemble code does not help. So my question is: anyone know how to use Xcode to debug Gromacs executable file? I need the breakpoints to be related with the source code so that I can trace the flow. As I commented in an email to Harold a little while back... There is no substitute for getting a debugger and stepping through a run of GROMACS built with CFLAGS=-g to understand the flow of the code. Symbolic information used by a debugger is added by the compiler and linker in response to an explicit request. I cast a quick eye over that tutorial, and didn't see it mention this point, so Xcode must be doing some magic behind the scenes that doesn't serve to educate the user. So, setting the CFLAGS environment variable as above, or using ./configure --your-options CFLAGS=-g -anyotheroptions will provide the symbolic information. 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
Re: [gmx-users] minimization
Morteza Khabiri wrote: Dear users I have a dimer protein which I want to minimized it..unfortunately the protein is in high energy level and before starting to minimize it explode. I already went through users email and also wiki gromacs and also I tried all the way like changing time step, change coulomb type ,... but they did not work .. As MARK suggest me I try to minimize monomer separately but the monomers itself also have high energy and it is not possible to minimize them... OK, so simplify further to find the problem. Minimize just one half of a monomer, etc. Consider writing a script to run the minimization to make this process fast. Remember to look at the structures to identify obvious problems. Mark I change the forcefield from olps to gromacs and minimization work. I did several minimization by gromacs forcefiled and then I tried to minimized the system by OPLS but again the system start exploiding... Is there any idea that why the minimization work by gromacs but not work with opls? finally I should simulate my system by opls and if I want to do it my system still not minimized for OPLS I will apprecite if there will be some idea for my problem 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] bad bond in polymer
Hi, the bad bond appear in the topology (.top) file. veduardo. Lab. de Fisicoquímica Molecular Facultas de Ciencias Universidad de Chile From: nicegromacs Sent: Wednesday, August 12, 2009 8:28 PM To: gmx-users@gromacs.org Subject: [gmx-users] bad bond in polymer Hi gmx-users, I am building a polymer and I've added the monomer unit to the .rtp file. The final structure appears with an undesired bond between the monomer units at the extremes of the polymer. How can I prevent the monomers at the end forming the bond? I have read other post like http://www.mail-archive.com/gmx-users@gromacs.org/msg21133.html but can not avoid this problem . Thank you in advance veduardo. Lab. de Fisicoquímica Molecular Facultas de Ciencias Universidad de Chile ___ 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] bad bond in polymer
nicegromacs wrote: Hi, the bad bond appear in the topology (.top) file. Then it is something you have added. If you want any useful advice, post the .rtp entries you are using. -Justin veduardo. Lab. de Fisicoquímica Molecular Facultas de Ciencias Universidad de Chile *From:* nicegromacs mailto:nicegrom...@live.cl *Sent:* Wednesday, August 12, 2009 8:28 PM *To:* gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Subject:* [gmx-users] bad bond in polymer Hi gmx-users, I am building a polymer and I've added the monomer unit to the .rtp file. The final structure appears with an undesired bond between the monomer units at the extremes of the polymer. How can I prevent the monomers at the end forming the bond? I have read other post like http://www.mail-archive.com/gmx-users@gromacs.org/msg21133.html but can not avoid this problem . Thank you in advance veduardo. Lab. de Fisicoquímica Molecular Facultas de Ciencias Universidad de Chile ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] Determining the energy of an individual atom
Darrell Koskinen wrote: Hi Mark, I do have a paper in my possession that provides a first principles calculation of the adsorption energy of ammonia on graphene. I was planning on using this paper to compare the adsorption energy to the vibrational energy of the individual atoms in the graphene lattice. But how do I measure the average kinetic energy of a graphene atom in my system? Well you'll need to have recorded velocities (nstvout) and use one or other of the utility programs to analyze your .trr. See manual 7.4 to see what might be useful, and then relevant sections of Appendix D. And I should also let you know that I have removed the ad hoc parameters and am using ffoplsaa in its pure unmodified form. That's a good start! :-) Mark Thanks again for your help. Darrell Date: Wed, 12 Aug 2009 13:42:08 +1000 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] Determining the energy of an individual atom. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4a823a10.6010...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed Darrell Koskinen wrote: Dear GROMACS Gurus, In my simulation of a graphene structure surrounded by an ammonia gas, I am not seeing any adsorption of the ammonia molecules onto the surface of the graphene structure. I am wondering if the reason I am not seeing any absorption is because the graphene lattice is vibrating and thereby imparting too much energy to the ammonia molecule when it comes into the vicinity of the graphene lattice, thus impairing any adsorption. I assume that the adsorption energy would have to be significantly greater than the vibrational energy in order to allow adsorption to occur. If this is true, then is there some way of determining the translational (vibrational) energy of an atom in the graphene lattice so that I may compare it to the adsorption energy? You can measure the average kinetic energy of an atom, but whether you can infer anything else might depend on comparing with a structure to which something did adsorb. Frankly, it seems rather more likely that the ad hoc combination of parameters you have described in the past is incapable of modelling this behaviour. Parameterization is only known to be useful within a limited domain. You might be able to demonstrate transferability, but it cannot be assumed. 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 ___ 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 installing gromacs
st wrote: Hi There, I have some problems installing gromacs on the linux server. fftw installed with no error, but when I install gromacs, I got the following error: * /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/home/y1gao/soft/fftw/lib -o grompp grompp.o libgmxpreprocess_d.la ../mdlib/l cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o .libs/grompp grompp.o -L/home/y1gao/soft/fftw/lib ./.libs/libgmxpreprocess_d.a -L/usr/X11R6/lib ../mdlib/.libs/libmd_d.so /n _d.so -lnsl -lfftw3 -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/home/y1gao/soft/gromacs//lib ../mdlib/.libs/libmd_d.so: undefined reference to `__libm_sse2_sincos' ../mdlib/.libs/libmd_d.so: undefined reference to `__libm_sse2_log' ../mdlib/.libs/libmd_d.so: undefined reference to `_intel_fast_memcpy' collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src' make: *** [all-recursive] Error 1 *** I used the combinations of the following fftw and gromacs: fftw 3.2.1; fftw3.2.2 gromacs 3.3.3; gromacs 4.0.4 gcc version 3.4.6 Actually it looks to me like you're using an Intel C compiler, not gcc. Set CC=gcc on the configure line. Mark The command I used are: * To install fftw: $ ./configure --enable-threads --enable-sse2 -prefix /home/y1gao/soft/fftw/lib $ make $ make install To install gromacs: $ ./configure --enable-shared LDFLAGS='-L/home/y1gao/soft/fftw/lib' CPPFLAGS='-I/home/y1gao/soft/fftw/include' --enable-double --prefix=/home/y1gao/soft/gromacs/ $ make $ make install ( error comes out here) * Could anyone help me find a way out? Thanks in advance. Stone ___ 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] bad bond in polymer
Hi, the .rtp [ POL ] [ atoms ] CAA CH30.000 CAB CH20.000 CAC CH20.000 CAD CH20.000 CAE CH20.000 CAF CH20.000 CAG CH10.000 CAH CH20.041 CAI CH10.107 CAJC0.352 OAK OM -0.750 OAL OM -0.750 CAM CH20.044 CANC0.373 OAO OM -0.709 OAP OM -0.708 [ bonds ] CAA CAB CAB CAC CAC CAD CAD CAE CAE CAF CAF CAG CAG CAH CAH CAI CAI CAJ CAI CAM CAJ OAK CAJ OAL CAM CAN CAN OAO CAN OAP CAG -CAM [ impropers ] CAG CAF -CAM CAH -CAM -CAN -CAI CAG CAJ CAI OAL OAK CAN CAM OAP OAO CAI CAH CAJ CAM -- From: Justin A. Lemkul jalem...@vt.edu Sent: Wednesday, August 12, 2009 9:23 PM To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] bad bond in polymer nicegromacs wrote: Hi, the bad bond appear in the topology (.top) file. Then it is something you have added. If you want any useful advice, post the .rtp entries you are using. -Justin veduardo. Lab. de Fisicoquímica Molecular Facultas de Ciencias Universidad de Chile *From:* nicegromacs mailto:nicegrom...@live.cl *Sent:* Wednesday, August 12, 2009 8:28 PM *To:* gmx-users@gromacs.org mailto:gmx-users@gromacs.org *Subject:* [gmx-users] bad bond in polymer Hi gmx-users, I am building a polymer and I've added the monomer unit to the .rtp file. The final structure appears with an undesired bond between the monomer units at the extremes of the polymer. How can I prevent the monomers at the end forming the bond? I have read other post like http://www.mail-archive.com/gmx-users@gromacs.org/msg21133.html but can not avoid this problem . Thank you in advance veduardo. Lab. de Fisicoquímica Molecular Facultas de Ciencias Universidad de Chile ___ 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 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] bad bond in polymer
nicegromacs wrote: CAG -CAM Defining a bond to a previous residue will certainly fail for at least one terminus of your polymer chain. You may find this post useful: http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html If things still aren't working, please post the structure file, as well, and identify the bond that is being formed that shouldn't. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users 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] PMF for membrane protein dimer
I am working with a membrane protein dimer, each monomer being constituted of a single helix. I have already studied the effect of point mutations on the structure and the free energy involved by using FEP. But I have read a paper in which the author has done PMF calculations in order to calculate the free energy of dimerization. In this paper (ref J. Am. Chem. Soc., 2005, 127 (23), pp 8478–8484) the author describes a system that is quite similar to mine, though he uses NAMD to do obtain the trajectories. I have tried gathering some information on this particular method (PMF) in gromacs and have found very little information regarding PFM being used to separate protein dimers or even separating system containing more than a dozen atoms or so. If I understood correctly, I am supposed to pull the two structures apart, and associate a lambda value for each distance I obtain. Well, I am a little bit lost here, since I did not really understand how is the pull code linked with the free energy calculation. I even found the two argon PMF tutorial quite confusing, since I do not see how I would obtain a restrain for the monomers in such a big system. So, for now I would like some information on how to obtain this kind of practical information (tutorials, instructions, articles etc). I know everyone is quite busy solving their own problems, so any direction now would help me have more specific doubts so that I can further address this list with more useful questions. Thank you Fabrício Bracht ___ 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] bad bond in polymer
Well, I tried to build a polymer with 3 monomers, DRG DR0 and DR1. In the pdb file They have the same order (DRG DR0 DR1). But when tried with pdb2gmx then I have the error: Fatal error: In the .rtp file in residue DR1 at line: CF1 CH3 0 1 I changed the order of monomers to DR0 DRG DR1 with respect to the ''head'' monomer (DR0), Monomer of in the middle (DRG), and tail monomer (DR1), and the error no change. I have not changed the .hdb file. the estructure.ent HETATM1 CAA DRG 1 58.110 44.852 36.809 HETATM2 CAB DRG 1 56.934 44.517 35.875 HETATM3 CAC DRG 1 56.190 45.811 35.500 HETATM4 CAD DRG 1 55.051 45.476 34.520 HETATM5 CAE DRG 1 54.318 46.770 34.118 HETATM6 CAF DRG 1 53.310 46.438 33.003 HETATM7 CAG DRG 1 52.657 47.686 32.473 HETATM8 CAH DRG 1 53.521 48.753 31.851 HETATM9 CAI DRG 1 54.199 48.265 30.599 HETATM 10 CAJ DRG 1 55.615 47.887 30.630 HETATM 11 OAK DRG 1 56.231 47.370 29.495 HETATM 12 OAL DRG 1 56.359 48.028 31.798 HETATM 13 CAM DRG 1 53.423 48.169 29.314 HETATM 14 CAN DRG 1 52.529 46.963 29.306 HETATM 15 OAO DRG 1 53.058 45.698 29.542 HETATM 16 OAP DRG 1 51.206 47.090 28.902 HETATM 17 CA1 DR0 1 43.743 50.975 25.947 HETATM 18 CA2 DR0 1 44.674 51.739 26.906 HETATM 19 CA3 DR0 1 45.313 50.749 27.897 HETATM 20 CA4 DR0 1 46.248 51.508 28.856 HETATM 21 CA5 DR0 1 46.862 50.512 29.856 HETATM 22 CA6 DR0 1 47.789 51.264 30.830 HETATM 23 CA7 DR0 1 48.356 50.315 31.851 HETATM 24 CA8 DR0 1 49.361 49.293 31.385 HETATM 25 CA9 DR0 1 50.545 49.110 32.302 HETATM 26 C10 DR0 1 51.122 50.259 33.020 HETATM 27 O12 DR0 1 50.919 51.560 32.571 HETATM 28 O11 DR0 1 51.877 50.069 34.174 HETATM 29 C13 DR0 1 51.189 47.782 32.378 HETATM 30 C14 DR0 1 50.382 46.559 32.210 HETATM 31 O16 DR0 1 50.972 45.336 31.910 HETATM 32 O15 DR0 1 48.997 46.595 32.315 HETATM 33 CF1 DR1 1 55.642 46.172 39.128 HETATM 34 CF2 DR1 1 54.229 46.780 39.194 HETATM 35 CF3 DR1 1 53.591 46.765 37.791 HETATM 36 CF4 DR1 1 52.185 47.384 37.876 HETATM 37 CF5 DR1 1 51.526 47.395 36.484 HETATM 38 CF6 DR1 1 50.134 48.044 36.601 HETATM 39 CF7 DR1 1 49.475 48.098 35.212 HETATM 40 CF8 DR1 1 48.132 48.846 35.298 HETATM 41 CF9 DR1 1 47.562 49.035 33.918 HETATM 42 C1F DR1 1 46.647 48.028 33.366 HETATM 43 O3F DR1 1 46.397 46.849 34.062 HETATM 44 O2F DR1 1 45.998 48.241 32.154 HETATM 45 C4F DR1 1 47.798 50.304 33.215 HETATM 46 C5F DR1 1 47.426 51.565 33.874 HETATM 47 O7F DR1 1 47.843 52.791 33.365 HETATM 48 O6F DR1 1 46.661 51.551 35.036 CONECT12 CONECT213 CONECT324 CONECT435 CONECT546 CONECT657 CONECT768 29 CONECT879 CONECT98 10 13 CONECT 109 11 12 CONECT 11 10 CONECT 12 10 CONECT 139 14 CONECT 14 13 15 16 CONECT 15 14 CONECT 16 14 CONECT 17 18 CONECT 18 17 19 CONECT 19 18 20 CONECT 20 19 21 CONECT 21 20 22 CONECT 22 21 23 CONECT 23 22 24 45 CONECT 24 23 25 CONECT 25 24 26 29 CONECT 26 25 27 28 CONECT 27 26 CONECT 28 26 CONECT 29 25 307 CONECT 30 29 31 32 CONECT 31 30 CONECT 32 30 CONECT 33 34 CONECT 34 33 35 CONECT 35 34 36 CONECT 36 35 37 CONECT 37 36 38 CONECT 38 37 39 CONECT 39 38 40 CONECT 40 39 41 CONECT 41 40 42 45 CONECT 42 41 43 44 CONECT 43 42 CONECT 44 42 CONECT 45 41 46 23 CONECT 46 45 47 48 CONECT 47 46 CONECT 48 46 END and the .rtp [ DRG ] ; unidad [ atoms ] CAA CH30.00 CAB CH20.00 CAC CH20.00 CAD CH20.00 CAE CH20.00 CAF CH20.00 CAG CH10.00 CAH CH20.04 CAI CH10.10 CAJC0.35 OAK OM -0.75 OAL OM -0.75 CAM CH20.04 CANC0.37 OAO OM -0.70 OAP OM -0.70 [ bonds ] CAM -CAG CAA CAB CAB CAC CAC CAD CAD CAE CAE CAF CAF CAG CAG CAH CAH CAI CAI CAJ CAI CAM CAJ OAK CAJ OAL CAM CAN CAN OAO CAN OAP CAG +CAM [ impropers ] CAG CAF -CAM C -CAM -CAN -CAI C CAJ CAI OAL O CAN CAM OAP O CAI CAH CAJ C [ DR0 ] ;head of [ atoms ] CA1 CH30.00 CA2 CH20.00 CA3 CH20.00 CA4 CH20.00 CA5 CH20.00 CA6 CH20.00 CA7 CH20.00 CA8 CH2
Re: [gmx-users] bad bond in polymer
Justin A. Lemkul wrote: nicegromacs wrote: CAG -CAM Defining a bond to a previous residue will certainly fail for at least one terminus of your polymer chain. You may find this post useful: http://oldwww.gromacs.org/pipermail/gmx-users/2009-March/040125.html I don't have any relevant experience, but the quoted .rtp might be using a technique suited for creating a circular/infinite polymer, which would cause the present problem. Finite polymers need capping residues, either explicitly defined, or using the .tdb mechanism. See chapter 5. 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
Re: [gmx-users] bad bond in polymer
nicegromacs wrote: Well, I tried to build a polymer with 3 monomers, DRG DR0 and DR1. In the pdb file They have the same order (DRG DR0 DR1). But when tried with pdb2gmx then I have the error: Fatal error: In the .rtp file in residue DR1 at line: CF1 CH3 0 1 There is no such line in the .rtp you provided. GROMACS would normally provide more diagnostic information than this. Are you reading it all? Are you using the right .rtp files? I changed the order of monomers to DR0 DRG DR1 with respect to the ''head'' monomer (DR0), Monomer of in the middle (DRG), and tail monomer (DR1), and the error no change. I have not changed the .hdb file. the estructure.ent HETATM1 CAA DRG 1 58.110 44.852 36.809 This first residue listed is named as for your repeating unit. You need to make sure the residue naming here matches your connectivity plan. Mark HETATM2 CAB DRG 1 56.934 44.517 35.875 HETATM3 CAC DRG 1 56.190 45.811 35.500 HETATM4 CAD DRG 1 55.051 45.476 34.520 HETATM5 CAE DRG 1 54.318 46.770 34.118 HETATM6 CAF DRG 1 53.310 46.438 33.003 HETATM7 CAG DRG 1 52.657 47.686 32.473 HETATM8 CAH DRG 1 53.521 48.753 31.851 HETATM9 CAI DRG 1 54.199 48.265 30.599 HETATM 10 CAJ DRG 1 55.615 47.887 30.630 HETATM 11 OAK DRG 1 56.231 47.370 29.495 HETATM 12 OAL DRG 1 56.359 48.028 31.798 HETATM 13 CAM DRG 1 53.423 48.169 29.314 HETATM 14 CAN DRG 1 52.529 46.963 29.306 HETATM 15 OAO DRG 1 53.058 45.698 29.542 HETATM 16 OAP DRG 1 51.206 47.090 28.902 HETATM 17 CA1 DR0 1 43.743 50.975 25.947 HETATM 18 CA2 DR0 1 44.674 51.739 26.906 HETATM 19 CA3 DR0 1 45.313 50.749 27.897 HETATM 20 CA4 DR0 1 46.248 51.508 28.856 HETATM 21 CA5 DR0 1 46.862 50.512 29.856 HETATM 22 CA6 DR0 1 47.789 51.264 30.830 HETATM 23 CA7 DR0 1 48.356 50.315 31.851 HETATM 24 CA8 DR0 1 49.361 49.293 31.385 HETATM 25 CA9 DR0 1 50.545 49.110 32.302 HETATM 26 C10 DR0 1 51.122 50.259 33.020 HETATM 27 O12 DR0 1 50.919 51.560 32.571 HETATM 28 O11 DR0 1 51.877 50.069 34.174 HETATM 29 C13 DR0 1 51.189 47.782 32.378 HETATM 30 C14 DR0 1 50.382 46.559 32.210 HETATM 31 O16 DR0 1 50.972 45.336 31.910 HETATM 32 O15 DR0 1 48.997 46.595 32.315 HETATM 33 CF1 DR1 1 55.642 46.172 39.128 HETATM 34 CF2 DR1 1 54.229 46.780 39.194 HETATM 35 CF3 DR1 1 53.591 46.765 37.791 HETATM 36 CF4 DR1 1 52.185 47.384 37.876 HETATM 37 CF5 DR1 1 51.526 47.395 36.484 HETATM 38 CF6 DR1 1 50.134 48.044 36.601 HETATM 39 CF7 DR1 1 49.475 48.098 35.212 HETATM 40 CF8 DR1 1 48.132 48.846 35.298 HETATM 41 CF9 DR1 1 47.562 49.035 33.918 HETATM 42 C1F DR1 1 46.647 48.028 33.366 HETATM 43 O3F DR1 1 46.397 46.849 34.062 HETATM 44 O2F DR1 1 45.998 48.241 32.154 HETATM 45 C4F DR1 1 47.798 50.304 33.215 HETATM 46 C5F DR1 1 47.426 51.565 33.874 HETATM 47 O7F DR1 1 47.843 52.791 33.365 HETATM 48 O6F DR1 1 46.661 51.551 35.036 CONECT12 CONECT213 CONECT324 CONECT435 CONECT546 CONECT657 CONECT768 29 CONECT879 CONECT98 10 13 CONECT 109 11 12 CONECT 11 10 CONECT 12 10 CONECT 139 14 CONECT 14 13 15 16 CONECT 15 14 CONECT 16 14 CONECT 17 18 CONECT 18 17 19 CONECT 19 18 20 CONECT 20 19 21 CONECT 21 20 22 CONECT 22 21 23 CONECT 23 22 24 45 CONECT 24 23 25 CONECT 25 24 26 29 CONECT 26 25 27 28 CONECT 27 26 CONECT 28 26 CONECT 29 25 307 CONECT 30 29 31 32 CONECT 31 30 CONECT 32 30 CONECT 33 34 CONECT 34 33 35 CONECT 35 34 36 CONECT 36 35 37 CONECT 37 36 38 CONECT 38 37 39 CONECT 39 38 40 CONECT 40 39 41 CONECT 41 40 42 45 CONECT 42 41 43 44 CONECT 43 42 CONECT 44 42 CONECT 45 41 46 23 CONECT 46 45 47 48 CONECT 47 46 CONECT 48 46 END and the .rtp [ DRG ] ; unidad [ atoms ] CAA CH30.00 CAB CH20.00 CAC CH20.00 CAD CH20.00 CAE CH20.00 CAF CH20.00 CAG CH10.00 CAH CH20.04 CAI CH10.10 CAJC0.35 OAK OM -0.75 OAL OM -0.75 CAM CH20.04 CANC0.37 OAO OM -0.70 OAP OM -0.70 [ bonds ] CAM -CAG CAA CAB CAB CAC CAC CAD CAD CAE CAE CAF CAF CAG CAG CAH CAH CAI CAI CAJ
Re: [gmx-users] problem installing gromacs
--- On Thu, 13/8/09, st y1...@ucsd.edu wrote: From: st y1...@ucsd.edu Subject: [gmx-users] problem installing gromacs To: gmx-users@gromacs.org Date: Thursday, 13 August, 2009, 1:42 AM Hi There, I have some problems installing gromacs on the linux server. fftw installed with no error, but when I install gromacs, I got the following error: * /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/home/y1gao/soft/fftw/lib -o grompp grompp.o libgmxpreprocess_d.la ../mdlib/l cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o .libs/grompp grompp.o -L/home/y1gao/soft/fftw/lib ./.libs/libgmxpreprocess_d.a -L/usr/X11R6/lib ../mdlib/.libs/libmd_d.so /n _d.so -lnsl -lfftw3 -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/home/y1gao/soft/gromacs//lib .../mdlib/.libs/libmd_d.so: undefined reference to `__libm_sse2_sincos' .../mdlib/.libs/libmd_d.so: undefined reference to `__libm_sse2_log' .../mdlib/.libs/libmd_d.so: undefined reference to `_intel_fast_memcpy' collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src' make: *** [all-recursive] Error 1 *** I used the combinations of the following fftw and gromacs: fftw 3.2.1; fftw3.2.2 gromacs 3.3.3; gromacs 4.0.4 gcc version 3.4.6 try with make links after make install of gromacs. probably this may help. good luck The command I used are: * To install fftw: $ ./configure --enable-threads --enable-sse2 -prefix /home/y1gao/soft/fftw/lib $ make $ make install To install gromacs: $ ./configure --enable-shared LDFLAGS='-L/home/y1gao/soft/fftw/lib' CPPFLAGS='-I/home/y1gao/soft/fftw/include' --enable-double --prefix=/home/y1gao/soft/gromacs/ $ make $ make install ( error comes out here) * Could anyone help me find a way out? Thanks in advance. Stone -Inline Attachment Follows- ___ 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 Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ 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 installing gromacs
Samik Bhattacharya wrote: --- On Thu, 13/8/09, st y1...@ucsd.edu wrote: From: st y1...@ucsd.edu Subject: [gmx-users] problem installing gromacs To: gmx-users@gromacs.org Date: Thursday, 13 August, 2009, 1:42 AM Hi There, I have some problems installing gromacs on the linux server. fftw installed with no error, but when I install gromacs, I got the following error: * /bin/sh ../../libtool --tag=CC --mode=link cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/home/y1gao/soft/fftw/lib -o grompp grompp.o libgmxpreprocess_d.la ../mdlib/l cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o .libs/grompp grompp.o -L/home/y1gao/soft/fftw/lib ./.libs/libgmxpreprocess_d.a -L/usr/X11R6/lib ../mdlib/.libs/libmd_d.so /n _d.so -lnsl -lfftw3 -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/home/y1gao/soft/gromacs//lib .../mdlib/.libs/libmd_d.so: undefined reference to `__libm_sse2_sincos' .../mdlib/.libs/libmd_d.so: undefined reference to `__libm_sse2_log' .../mdlib/.libs/libmd_d.so: undefined reference to `_intel_fast_memcpy' collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/nas/y1gao/installation_files/gromacs-4.0.4/gromacs-4.0.4/src' make: *** [all-recursive] Error 1 *** I used the combinations of the following fftw and gromacs: fftw 3.2.1; fftw3.2.2 gromacs 3.3.3; gromacs 4.0.4 gcc version 3.4.6 try with make links after make install of gromacs. probably this may help. good luck No. The object-linking process is failing. So making file system symlinks after object-linking and installation will not help. 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
[gmx-users] Exotic metal species
Der all, I'd like to know if any has had experience in using GROMACS for modeling exotic metal species like Gadolinium(III) and Indium(III)? My system is actually an Indium(III) ion coupled to DTPA (diethylenetriaminepentaacetate), an octadentate ligand forms bonds with metals through three atoms of nitrogen and five atoms of oxygen. I've consulted the Gromacs wiki ( http://www.gromacs.org/WIKI-import/Exotic_Species) and it suggests that I consult someone with expertise in this area. Has anyone had any (successful?) experience in this effort? Thanks, Lili ___ 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] error:Segmentation fault
Hello everyone I am doing MD on a protein, and everything including the EM seems to go well. When I start to do the position restrained MD (or even directly the MD without doing the PR MD), I get a Segmentation fault. when a doing EM,I set nsteps = 500,because i just want to go though the procedures,but there is a result: Steepest Descents did not converge to Fmax 1000 in 501 steps. i go on the grompp pr.mdp and mdrun command, Segmentation fault comes up.details as followed: Step -2, time -0.004 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.060225 (between atoms 4110 and 4112) rms 0.001990 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length starting mdrun 'CYP2W1_CYSHEME in water' 100 steps, 0.2 ps. Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: max 20.941092 (between atoms 4012 and 4013) rms 0.630786 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4008 4010 59.80.1470 0.2246 0.1470 4010 4011 87.30.1536 1.1098 0.1530 4010 4023 56.20.1530 0.2198 0.1530 so much atoms number Warning: 1-4 interaction between 4008 and 4012 at distance 1.404 which is larger than the 1-4 table size 1.000 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file Step 1, time 0.002 (ps) LINCS WARNING relative constraint deviation after LINCS: max 10879059641262569160704.00 (between atoms 4029 and 4030) rms 157073328433382031360.00 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 933935 38.70.1330 0.1811 0.1330 935936 41.30.1000 0.1411 0.1000 so much atoms number 4210 4212 52.30.1330 0.2032 0.1330 4212 4213 30.80.1000 0.1209 0.1000 Wrote pdb files with previous and current coordinates [localhost:09678] *** Process received signal *** [localhost:09678] Signal: Segmentation fault (11) [localhost:09678] Signal code: Address not mapped (1) [localhost:09678] Failing at address: 0x5ad01b00 [localhost:09678] [ 0] /lib/tls/libpthread.so.0 [0xab68b0] [localhost:09678] [ 1] mdrun(do_nonbonded+0x349) [0x816d4a1] [localhost:09678] *** End of error message *** Segmentation fault I have been trying to solve this problem for quite some time now. It would be very helpful if you can suggest some way to work around this problem. thanks! jianlu guo___ 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
