[gmx-users] installation

2009-06-01 Thread Samik Bhattacharya 
hi,I
 
i am facing a lot of troubles in installing Gromacs in my Redhat machine..I've 
followed all the instructions given in the manual as well as in the website. 
ialso have installed fftw,its compiling with no problem. . but whenever i run 
pdb2gmx or command lke that its giving an error "command not found". a little 
help regarding this matter will be very encouraging. 
thankx
 Shamik



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[gmx-users] Re: gmx-users Digest, Vol 62, Issue 4

2009-06-01 Thread Alan Chen 

Hi Rebeca:

If you wish to replicate the settings of 


http://pubs.acs.org/doi/abs/10.1021/jp0765392

(Aqvist's ions in AMBER) then you need the following LJ cross-types specified 
in your non-bonded forcefield or topology file, which were generated using 
geometric mixing rule instead of the (AMBER) additive mixing rule.

amber99_31 amber99_30  1  3.83554389e-01   7.56034201e-02 ;Na-Cl jorgensen 
CL
amber99_51 amber99_30  1  4.66877340e-01  2.60065255e-02 ;K-Cl jorgensen CL
amber99_53 amber99_30  1  5.44666722e-01  1.29237407e-02 ;Cs-Cl jorgensen CL
amber99_30 amber99_30  1  4.41724e-01 4.92833e-01  ;Cl-Cl (jorgensen)
amber99_31 amber99_31  1  3.33045e-01 1.1598e-02   ;Na-Na
amber99_51 amber99_51  1  4.93463e-01 1.37235e-02  ;K-K
amber99_53 amber99_53  1  6.716e-01   3.38904e-04  ;Cs-Cs

To clear up some possible confusion, it should be noted that recent OPLS 
forcefields include Aqvist's ions by default for use with simulations with 
TIP3P water, and the OPLS ion parameters others are referring to are officially 
considered obsolete. Jorgensen has also published ions for use with TIP4P using 
the Aqvist paradigm, although I do not have any experience using these 
parameters.

Hope it helps your aggregation problems!

Alan Chen


  
 
 
 > Date: Mon, 1 Jun 2009 14:52:35 -0300

 > Subject: RE: [gmx-users] crystals of KCl during simulation
 > From: mo...@ufscar.br
 > To: gmx-users@gromacs.org
 >
 > Hi Rebeca,
 >
 > I found out a few years ago that OPLS parameters for Na+ were inadequate
 > for my simulations on surfactants aggregation due to the formation of
 > stable (and unrealistic) ionic bridges. I got better structures using
 > Aqvist's parameters (available in GROMACS), maybe you could try these
 > parameters for K+ as well.
 >
 > please let me know if that works.
 >
 > best regards,
 >
 > André
 >
 >
 > >
 > > Yes, I use PME.
 > >
 > >> Date: Mon, 1 Jun 2009 19:34:27 +0200
 > >> From: sp...@xray.bmc.uu.se
 > >> To: gmx-users@gromacs.org
 > >> Subject: Re: [gmx-users] crystals of KCl during simulation
 > >>
 > >> Rebeca García Fandiño wrote:
 > >> > Thank you very much for your answer. I have read some recent
 > >> literature,
 > >> > and you are right, it is a problem about the parameters for ions in
 > >> Amber.
 > >> >
 > >> > I have found this paper:
 > >> > Parameters of Monovalent Ions in the Amber-99 Forcefield: 
Assesment of

 > >> > Inaccuracies and Proposed Improvements
 > >> > http://pubs.acs.org/doi/abs/10.1021/jp0765392
 > >> >
 > >> > There, they simulate nucleic acids using a combination of Amber and
 > >> > OPLS sigma and epsilon for the ions. I have tried that in the 
case of

 > >> my
 > >> > protein, just changing the ion sigma and epsilon in the topology by
 > >> > those corresponding to OPLS, but I still observe aggregation for the
 > >> ions.
 > >> >
 > >> > Would this combination of Amber and OPLS have any kind of potential
 > >> > problem during the simulation? Has anybody any idea to avoid 
this type

 > >> > of artefact?
 > >>
 > >> Just checking, do you use PME? (You should...)
 > >> >
 > >> > Thank you very much in advance,
 > >> >
 > >> > Rebeca.
 > >> >
 > >> > > To: gmx-users@gromacs.org
 > >> > > Subject: Re: [gmx-users] crystals of KCl during simulation
 > >> > > Date: Mon, 1 Jun 2009 14:34:55 +0200
 > >> > > From: baa...@smplinux.de
 > >> > >
 > >> > >
 > >> > > Hi,
 > >> > >
 > >> > > rega...@hotmail.com said:
 > >> > > >> [..] but after equilibration I have observed that KCl is
 > >> > aggregating, like
 > >> > > >> if it was making crystals. When I used NaCl instead KCl, 
this not

 > >> > > >> happened.
 > >> > >
 > >> > > >> Does anybody has any idea about the reason of the behaviour of
 > >> KCl in
 > >> > > >> the simulation?
 > >> > >
 > >> > > This even does happen with Amber :) So my guess is you correctly
 > >> > transferred
 > >> > > the parameters, but stumbled upon an artefact. If you check the
 > >> recent
 > >> > > literature you may notice that many publications with Amber 
using K+
 > >> > > only employ minimal (neutralising) salt conditions as a 
workaround.

 > >> At
 > >> > > least this is what we did recently [1].
 > >> > >
 > >> > > Marc Baaden
 > >> > >
 > >> > > [1] Interactions between neuronal fusion proteins explored by
 > >> molecular
 > >> > > dynamics, Biophys.J.94, 2008, 3436-3446.
 > >> > > http://dx.doi.org/10.1529/biophysj.107.123117
 > >> > >
 > >> > > --
 > >> > > 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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Re: [gmx-users] Fatal error:Library file aminoacids.dat not found in current dir nor in default directories

2009-06-01 Thread Mark Abraham 
Jinyao Wang wrote:
> Hi,gmx-users
> I am running a editconf commond like this,
> editconf_d -f *.gro -bt cubic -c -d 2.5 -o box.gro
> but I am getting the following the fatal error:
> Fatal error:
> Library file aminoacids.dat not found in current dir nor in default 
> directories.
> (You can set the directories to search with the GMXLIB path variable)
> How can I solve it?

See
http://wiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation

Mark
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[gmx-users] Fatal error:Library file aminoacids.dat not found in current dir nor in default directories

2009-06-01 Thread Jinyao Wang 
Hi,gmx-users
I am running a editconf commond like this,
editconf_d -f *.gro -bt cubic -c -d 2.5 -o box.gro
but I am getting the following the fatal error:
Fatal error:
Library file aminoacids.dat not found in current dir nor in default directories.
(You can set the directories to search with the GMXLIB path variable)
How can I solve it?
Thank you in advance



 Jinyao Wang  Ph.D. Candidate 
State Key Laboratory of Electroanalytical Chemistry
ChangChun Institute of Applied Chemistry (CIAC)
Chinese Academy of Sciences (CAS)
Address: 5625 Renmin Street, Changchun 130022, P.R. China
Tel.: +86-0431-85262609
Email:  wan...@ciacjl.cn
 
URL:   http://fyzhao.ciac.jl.cn
   http://www.ciac.jl.cn 
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Re: [gmx-users] crystals of KCl during simulation

2009-06-01 Thread David van der Spoel 

Rebeca García Fandiño wrote:


 Thank you very much, André. Could you please indicate me how could 
I use these parameters in Gromacs? I have not seen them included in 
ions.itp and I could not find anything in the manual.

Best wishes,
Rebeca.



I would recommend reading the following paper, even though it only is 
about NaCl it compares the properties of four different parameter sets, 
and IIRC Åqvist's parameters were not so great.


@Article{ Hess2006c,
  author =   "B. Hess and C. Holm and N. {van der Vegt}",
  title ="Osmotic coefficients of atomistic NaCl (aq) force
  fields",
  journal =  "J. Chem. Phys.",
  year = 2006,
  volume =   124,
  pages =164509,
  abstract = "Solvated ions are becoming increasingly important
  for (bio)molecular simulations. But there are not
  much suitable data to validate the
  intermediate-range solution structure that ion-water
  force fields produce. We compare six selected
  combinations of four biomolecular Na-Cl force fields
  and four popular water models by means of effective
  ion-ion potentials. First we derive an effective
  potential at high dilution from simulations of two
  ions in explicit water. At higher ionic
  concentration multibody effects will become
  important. We propose to capture those by employing
  a concentration dependent dielectric
  permittivity. With the so obtained effective
  potentials we then perform implicit solvent
  simulations. We demonstrate that our effective
  potentials accurately reproduce ion-ion coordination
  numbers and the local structure. They allow us
  furthermore to calculate osmotic coefficients that
  can be directly compared with experimental data. We
  show that the osmotic coefficient is a sensitive and
  accurate measure for the effective ion-ion
  interactions and the intermediate-range structure of
  the solution. It is therefore a suitable and useful
  quantity for validating and parametrizing atomistic
  ion-water force fields. (c) 2006 American Institute
  of Physics. 0021-9606"
}



 
 
 > Date: Mon, 1 Jun 2009 14:52:35 -0300

 > Subject: RE: [gmx-users] crystals of KCl during simulation
 > From: mo...@ufscar.br
 > To: gmx-users@gromacs.org
 >
 > Hi Rebeca,
 >
 > I found out a few years ago that OPLS parameters for Na+ were inadequate
 > for my simulations on surfactants aggregation due to the formation of
 > stable (and unrealistic) ionic bridges. I got better structures using
 > Aqvist's parameters (available in GROMACS), maybe you could try these
 > parameters for K+ as well.
 >
 > please let me know if that works.
 >
 > best regards,
 >
 > André
 >
 >
 > >
 > > Yes, I use PME.
 > >
 > >> Date: Mon, 1 Jun 2009 19:34:27 +0200
 > >> From: sp...@xray.bmc.uu.se
 > >> To: gmx-users@gromacs.org
 > >> Subject: Re: [gmx-users] crystals of KCl during simulation
 > >>
 > >> Rebeca García Fandiño wrote:
 > >> > Thank you very much for your answer. I have read some recent
 > >> literature,
 > >> > and you are right, it is a problem about the parameters for ions in
 > >> Amber.
 > >> >
 > >> > I have found this paper:
 > >> > Parameters of Monovalent Ions in the Amber-99 Forcefield: 
Assesment of

 > >> > Inaccuracies and Proposed Improvements
 > >> > http://pubs.acs.org/doi/abs/10.1021/jp0765392
 > >> >
 > >> > There, they simulate nucleic acids using a combination of Amber and
 > >> > OPLS sigma and epsilon for the ions. I have tried that in the 
case of

 > >> my
 > >> > protein, just changing the ion sigma and epsilon in the topology by
 > >> > those corresponding to OPLS, but I still observe aggregation for the
 > >> ions.
 > >> >
 > >> > Would this combination of Amber and OPLS have any kind of potential
 > >> > problem during the simulation? Has anybody any idea to avoid 
this type

 > >> > of artefact?
 > >>
 > >> Just checking, do you use PME? (You should...)
 > >> >
 > >> > Thank you very much in advance,
 > >> >
 > >> > Rebeca.
 > >> >
 > >> > > To: gmx-users@gromacs.org
 > >> > > Subject: Re: [gmx-users] crystals of KCl during simulation
 > >> > > Date: Mon, 1 Jun 2009 14:34:55 +0200
 > >> > > From: baa...@smplinux.de
 > >> > >
 > >> > >
 > >> > > Hi,
 > >> > >
 > >> > > rega...@hotmail.com said:
 > >> > > >> [..] but after equilibration I have observed that KCl is
 > >> > aggregating, like
 > >> > > >> if it was making crystals. When I used NaCl instead KCl, 
this not

 > >> > > >> happened.
 > >> > >
 > >> > > >> Does anybody has any idea about the reason of the behaviour of
 > >> KCl in
 > >> > > >> the simulation?
 > >> > >
 > >> >

RE: [gmx-users] crystals of KCl during simulation

2009-06-01 Thread Rebeca García Fandiño 


 Thank you very much, André. Could you please indicate me how could I use these 
parameters in Gromacs? I have not seen them included in ions.itp and I could 
not find anything in the manual.

Best wishes,

Rebeca.

 

 
> Date: Mon, 1 Jun 2009 14:52:35 -0300
> Subject: RE: [gmx-users] crystals of KCl during simulation
> From: mo...@ufscar.br
> To: gmx-users@gromacs.org
> 
> Hi Rebeca,
> 
> I found out a few years ago that OPLS parameters for Na+ were inadequate
> for my simulations on surfactants aggregation due to the formation of
> stable (and unrealistic) ionic bridges. I got better structures using
> Aqvist's parameters (available in GROMACS), maybe you could try these
> parameters for K+ as well.
> 
> please let me know if that works.
> 
> best regards,
> 
> André
> 
> 
> >
> > Yes, I use PME.
> >
> >> Date: Mon, 1 Jun 2009 19:34:27 +0200
> >> From: sp...@xray.bmc.uu.se
> >> To: gmx-users@gromacs.org
> >> Subject: Re: [gmx-users] crystals of KCl during simulation
> >>
> >> Rebeca García Fandiño wrote:
> >> > Thank you very much for your answer. I have read some recent
> >> literature,
> >> > and you are right, it is a problem about the parameters for ions in
> >> Amber.
> >> >
> >> > I have found this paper:
> >> > Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of
> >> > Inaccuracies and Proposed Improvements
> >> > http://pubs.acs.org/doi/abs/10.1021/jp0765392
> >> >
> >> > There, they simulate nucleic acids using a combination of Amber and
> >> > OPLS sigma and epsilon for the ions. I have tried that in the case of
> >> my
> >> > protein, just changing the ion sigma and epsilon in the topology by
> >> > those corresponding to OPLS, but I still observe aggregation for the
> >> ions.
> >> >
> >> > Would this combination of Amber and OPLS have any kind of potential
> >> > problem during the simulation? Has anybody any idea to avoid this type
> >> > of artefact?
> >>
> >> Just checking, do you use PME? (You should...)
> >> >
> >> > Thank you very much in advance,
> >> >
> >> > Rebeca.
> >> >
> >> > > To: gmx-users@gromacs.org
> >> > > Subject: Re: [gmx-users] crystals of KCl during simulation
> >> > > Date: Mon, 1 Jun 2009 14:34:55 +0200
> >> > > From: baa...@smplinux.de
> >> > >
> >> > >
> >> > > Hi,
> >> > >
> >> > > rega...@hotmail.com said:
> >> > > >> [..] but after equilibration I have observed that KCl is
> >> > aggregating, like
> >> > > >> if it was making crystals. When I used NaCl instead KCl, this not
> >> > > >> happened.
> >> > >
> >> > > >> Does anybody has any idea about the reason of the behaviour of
> >> KCl in
> >> > > >> the simulation?
> >> > >
> >> > > This even does happen with Amber :) So my guess is you correctly
> >> > transferred
> >> > > the parameters, but stumbled upon an artefact. If you check the
> >> recent
> >> > > literature you may notice that many publications with Amber using K+
> >> > > only employ minimal (neutralising) salt conditions as a workaround.
> >> At
> >> > > least this is what we did recently [1].
> >> > >
> >> > > Marc Baaden
> >> > >
> >> > > [1] Interactions between neuronal fusion proteins explored by
> >> molecular
> >> > > dynamics, Biophys.J.94, 2008, 3436-3446.
> >> > > http://dx.doi.org/10.1529/biophysj.107.123117
> >> > >
> >> > > --
> >> > > 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
> >> > >
> >> > >
> >> > > ___
> >> > > 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
> >> >
> >> > 
> >> > ¿Eres del Madrid, del Barça, del Atleti...? Apoya a tu equipo en la
> >> Zona
> >> > Fan de MSN Deportes
> >> > 
> >> >
> >> >
> >> > 
> >> >
> >> > ___
> >> > 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
> >>
> >>
> >> --
> >> David.
> >> 
> >> David van der Spoel, PhD, Professor of Biology
> >> Dept. of Cell and Molecular B

RE: [gmx-users] crystals of KCl during simulation

2009-06-01 Thread moura 
Hi Rebeca,

I found out a few years ago that OPLS parameters for Na+ were inadequate
for my simulations on surfactants aggregation due to the formation of
stable (and unrealistic) ionic bridges. I got better  structures using
Aqvist's parameters (available in GROMACS), maybe you could try these
parameters for K+ as well.

please let me know if that works.

best regards,

André


>
> Yes, I use PME.
>
>> Date: Mon, 1 Jun 2009 19:34:27 +0200
>> From: sp...@xray.bmc.uu.se
>> To: gmx-users@gromacs.org
>> Subject: Re: [gmx-users] crystals of KCl during simulation
>>
>> Rebeca García Fandiño wrote:
>> > Thank you very much for your answer. I have read some recent
>> literature,
>> > and you are right, it is a problem about the parameters for ions in
>> Amber.
>> >
>> > I have found this paper:
>> > Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of
>> > Inaccuracies and Proposed Improvements
>> > http://pubs.acs.org/doi/abs/10.1021/jp0765392
>> >
>> > There, they simulate nucleic acids using a combination of Amber and
>> > OPLS sigma and epsilon for the ions. I have tried that in the case of
>> my
>> > protein, just changing the ion sigma and epsilon in the topology by
>> > those corresponding to OPLS, but I still observe aggregation for the
>> ions.
>> >
>> > Would this combination of Amber and OPLS have any kind of potential
>> > problem during the simulation? Has anybody any idea to avoid this type
>> > of artefact?
>>
>> Just checking, do you use PME? (You should...)
>> >
>> > Thank you very much in advance,
>> >
>> > Rebeca.
>> >
>> > > To: gmx-users@gromacs.org
>> > > Subject: Re: [gmx-users] crystals of KCl during simulation
>> > > Date: Mon, 1 Jun 2009 14:34:55 +0200
>> > > From: baa...@smplinux.de
>> > >
>> > >
>> > > Hi,
>> > >
>> > > rega...@hotmail.com said:
>> > > >> [..] but after equilibration I have observed that KCl is
>> > aggregating, like
>> > > >> if it was making crystals. When I used NaCl instead KCl, this not
>> > > >> happened.
>> > >
>> > > >> Does anybody has any idea about the reason of the behaviour of
>> KCl in
>> > > >> the simulation?
>> > >
>> > > This even does happen with Amber :) So my guess is you correctly
>> > transferred
>> > > the parameters, but stumbled upon an artefact. If you check the
>> recent
>> > > literature you may notice that many publications with Amber using K+
>> > > only employ minimal (neutralising) salt conditions as a workaround.
>> At
>> > > least this is what we did recently [1].
>> > >
>> > > Marc Baaden
>> > >
>> > > [1] Interactions between neuronal fusion proteins explored by
>> molecular
>> > > dynamics, Biophys.J.94, 2008, 3436-3446.
>> > > http://dx.doi.org/10.1529/biophysj.107.123117
>> > >
>> > > --
>> > > 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
>> > >
>> > >
>> > > ___
>> > > 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
>> >
>> > 
>> > ¿Eres del Madrid, del Barça, del Atleti...? Apoya a tu equipo en la
>> Zona
>> > Fan de MSN Deportes
>> > 
>> >
>> >
>> > 
>> >
>> > ___
>> > 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
>>
>>
>> --
>> David.
>> 
>> David van der Spoel, PhD, Professor of Biology
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>> phone: 46 18 471 4205 fax: 46 18 511 755
>> sp...@xray.bmc.uu.se sp...@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!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>>

RE: [gmx-users] crystals of KCl during simulation

2009-06-01 Thread Rebeca García Fandiño 

Yes, I use PME.
 
> Date: Mon, 1 Jun 2009 19:34:27 +0200
> From: sp...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] crystals of KCl during simulation
> 
> Rebeca García Fandiño wrote:
> > Thank you very much for your answer. I have read some recent literature, 
> > and you are right, it is a problem about the parameters for ions in Amber.
> > 
> > I have found this paper:
> > Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of 
> > Inaccuracies and Proposed Improvements
> > http://pubs.acs.org/doi/abs/10.1021/jp0765392
> > 
> > There, they simulate nucleic acids using a combination of Amber and 
> > OPLS sigma and epsilon for the ions. I have tried that in the case of my 
> > protein, just changing the ion sigma and epsilon in the topology by 
> > those corresponding to OPLS, but I still observe aggregation for the ions.
> > 
> > Would this combination of Amber and OPLS have any kind of potential 
> > problem during the simulation? Has anybody any idea to avoid this type 
> > of artefact?
> 
> Just checking, do you use PME? (You should...)
> > 
> > Thank you very much in advance,
> > 
> > Rebeca.
> > 
> > > To: gmx-users@gromacs.org
> > > Subject: Re: [gmx-users] crystals of KCl during simulation
> > > Date: Mon, 1 Jun 2009 14:34:55 +0200
> > > From: baa...@smplinux.de
> > >
> > >
> > > Hi,
> > >
> > > rega...@hotmail.com said:
> > > >> [..] but after equilibration I have observed that KCl is 
> > aggregating, like
> > > >> if it was making crystals. When I used NaCl instead KCl, this not
> > > >> happened.
> > >
> > > >> Does anybody has any idea about the reason of the behaviour of KCl in
> > > >> the simulation?
> > >
> > > This even does happen with Amber :) So my guess is you correctly 
> > transferred
> > > the parameters, but stumbled upon an artefact. If you check the recent
> > > literature you may notice that many publications with Amber using K+
> > > only employ minimal (neutralising) salt conditions as a workaround. At
> > > least this is what we did recently [1].
> > >
> > > Marc Baaden
> > >
> > > [1] Interactions between neuronal fusion proteins explored by molecular
> > > dynamics, Biophys.J.94, 2008, 3436-3446.
> > > http://dx.doi.org/10.1529/biophysj.107.123117
> > >
> > > --
> > > 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
> > >
> > >
> > > ___
> > > 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!
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> > 
> > ¿Eres del Madrid, del Barça, del Atleti...? Apoya a tu equipo en la Zona 
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> > 
> > 
> > 
> > 
> > 
> > ___
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> -- 
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> 
> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se
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Re: [gmx-users] crystals of KCl during simulation

2009-06-01 Thread David van der Spoel 

Rebeca García Fandiño wrote:
Thank you very much for your answer. I have read some recent literature, 
and you are right, it is a problem about the parameters for ions in Amber.
 
I have found this paper:
Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of 
Inaccuracies and Proposed Improvements

http://pubs.acs.org/doi/abs/10.1021/jp0765392
 
There, they simulate nucleic acids using a combination of Amber and 
OPLS sigma and epsilon for the ions. I have tried that in the case of my 
protein, just changing the ion sigma and epsilon in the topology by 
those corresponding to OPLS, but I still observe aggregation for the ions.
 
Would this combination of Amber and OPLS have any kind of potential 
problem during the simulation? Has anybody any idea to avoid this type 
of artefact?


Just checking, do you use PME? (You should...)
 
Thank you very much in advance,
 
Rebeca.
 
 > To: gmx-users@gromacs.org

 > Subject: Re: [gmx-users] crystals of KCl during simulation
 > Date: Mon, 1 Jun 2009 14:34:55 +0200
 > From: baa...@smplinux.de
 >
 >
 > Hi,
 >
 > rega...@hotmail.com said:
 > >> [..] but after equilibration I have observed that KCl is 
aggregating, like

 > >> if it was making crystals. When I used NaCl instead KCl, this not
 > >> happened.
 >
 > >> Does anybody has any idea about the reason of the behaviour of KCl in
 > >> the simulation?
 >
 > This even does happen with Amber :) So my guess is you correctly 
transferred

 > the parameters, but stumbled upon an artefact. If you check the recent
 > literature you may notice that many publications with Amber using K+
 > only employ minimal (neutralising) salt conditions as a workaround. At
 > least this is what we did recently [1].
 >
 > Marc Baaden
 >
 > [1] Interactions between neuronal fusion proteins explored by molecular
 > dynamics, Biophys.J.94, 2008, 3436-3446.
 > http://dx.doi.org/10.1529/biophysj.107.123117
 >
 > --
 > 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
 >
 >
 > ___
 > 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


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--
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David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  46 18 471 4205  fax: 46 18 511 755
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se

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RE: [gmx-users] crystals of KCl during simulation

2009-06-01 Thread Rebeca García Fandiño 

Thank you very much for your answer. I have read some recent literature, and 
you are right, it is a problem about the parameters for ions in Amber.

 

I have found this paper:

Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of 
Inaccuracies and Proposed Improvements

http://pubs.acs.org/doi/abs/10.1021/jp0765392

 

There, they simulate nucleic acids using a combination of Amber and OPLS sigma 
and epsilon for the ions. I have tried that in the case of my protein, just 
changing the ion sigma and epsilon in the topology by those corresponding to 
OPLS, but I still observe aggregation for the ions.

 

Would this combination of Amber and OPLS have any kind of potential problem 
during the simulation? Has anybody any idea to avoid this type of artefact?

 

Thank you very much in advance,

 

Rebeca.
 
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] crystals of KCl during simulation 
> Date: Mon, 1 Jun 2009 14:34:55 +0200
> From: baa...@smplinux.de
> 
> 
> Hi,
> 
> rega...@hotmail.com said:
> >> [..] but after equilibration I have observed that KCl is aggregating, like
> >> if it was making crystals. When I used NaCl instead KCl, this not
> >> happened.
> 
> >> Does anybody has any idea about the reason of the behaviour of KCl in
> >> the simulation?
> 
> This even does happen with Amber :) So my guess is you correctly transferred
> the parameters, but stumbled upon an artefact. If you check the recent 
> literature you may notice that many publications with Amber using K+ 
> only employ minimal (neutralising) salt conditions as a workaround. At 
> least this is what we did recently [1].
> 
> Marc Baaden
> 
> [1] Interactions between neuronal fusion proteins explored by molecular
> dynamics, Biophys.J.94, 2008, 3436-3446.
> http://dx.doi.org/10.1529/biophysj.107.123117
> 
> -- 
> 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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[gmx-users] Extend water layer along negative Z-direction

2009-06-01 Thread Chris Neale 

Hi Anirban,

I suspect that your problem is that you define a box with zero x, zero y, and a 
negative z. I think it's time to read the manual.

Hi ALL,

Thanks a lot Chris, Justin and Tsjerk for yor replies.
Actually, my problem is not fully resolved. A portion of the protein tail is outside the 
water box in the Z direction (coordinate in Z is -35). So as suggested by you when I am 
issuing the command "editconf -f box.gro -o BOX.gro -box 0 0 -3.5", but after 
that genbox is giving the error:

Fatal error:
Undefined solute box.
Create one with editconf or give explicit -box command line option

Please can you specify the proper command, so that the water box is extended 
only in the negative Z direction (to solvate the portion of the protein out of 
the box)

Regards,

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Re: [gmx-users] crystals of KCl during simulation

2009-06-01 Thread Marc Baaden 

Hi,

rega...@hotmail.com said:
>> [..] but after equilibration I have observed that KCl is aggregating, like
>> if it was making crystals. When I used NaCl instead KCl, this not
>> happened.

>> Does anybody has any idea about the reason of the behaviour of KCl in
>> the simulation?

This even does happen with Amber :)  So my guess is you correctly transferred
the parameters, but stumbled upon an artefact. If you check the recent 
literature you may notice that many publications with Amber using K+ 
only employ minimal (neutralising) salt conditions as a workaround. At 
least this is what we did recently [1].

Marc Baaden

[1] Interactions between neuronal fusion proteins explored by molecular
dynamics, Biophys.J.94, 2008, 3436-3446.
http://dx.doi.org/10.1529/biophysj.107.123117

-- 
 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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Re: [gmx-users] crystals of KCl during simulation

2009-06-01 Thread Mark Abraham 

Rebeca García Fandiño wrote:

Hi,
I am trying to simulate a protein in aqueous solution 1M (KCl) with 
Gromacs and using the amber force field.


I get the topology of the solvated protein - without the ions- from 
amber (Leap) and then used the script amb2gmx.pl to obtain the Gromacs 
.top and .gro files.
I did not introduced the ions from Amber because amb2gmx.pl is only 
written for NaCl, so I used genion to ionize the system.

I added the lines correspondent to the ions in Amber to the .top of Gromacs:

[ atomtypes ]
amber99_51 K  0.  0.  A   4.73602e-01  1.37235e-03 ; K+ ion
amber99_30Cl  0.  0.  A   4.40104e-01  4.18400e-01 ; Cl- ion

[ moleculetype ]
; molname   nrexcl
K   1

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
 1  amber99_51  1K  K   1   1   39.1

[ moleculetype ]
; molname   nrexcl
Cl  1

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
 1  amber99_30  1Cl Cl  1  -1   35.45000

and everything went OK, but after equilibration I have observed that KCl 
is aggregating, like if it was making crystals. When I used NaCl instead 
KCl, this not happened.


Does anybody has any idea about the reason of the behaviour of KCl in 
the simulation?


You may have supplied LJ parameters that are not appropriate for the LJ 
 type and combination rule in force. Compare the magnitudes of the 
final two parameters with the other ffamber ion [ atomtype ] entries. 
Also see header section of ffamber.itp and relevant manual sections.


Mark
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Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization

2009-06-01 Thread Mark Abraham 

Stefano Meliga wrote:

Hi again,

The energy minimization with conjugate gradient integrator still gives 
me two warnings of the type:


t = 0.011 ps: Water molecule starting at atom 28122 can not be settled.
Check for bad contacts and/or reduce the timestep.


OK I checked the code, and reporting a timestep is erroneous. Apologies 
for my misleading advice earlier. I filed a bugzilla about the message. 
It likely should read "Step 11: Water molecule..."


Nonetheless, the water at around 28122 may have had a serious problem 
that is worth checking out, lest something break later on in the simulation.


Mark


My command lines are:

$grxdir/grompp -f 4AKEpreEMcg.mdp -po 4AKE_EMcg.mdp -c 4AKE_EMsteep.gro 
-p 4AKEallHion.top -pp 4AKEpreEMsteep.top -o 4AKE_EMcg.tpr
$grxdir/mdrun -s 4AKE_EMcg.tpr -o 4AKE_EMcg.trr -c 4AKE_EMcg.gro -e 
4AKE_EMcg.edr -g 4AKE_EMcg.log -v


This is my mdp file 4AKEpreEMcg.mdp:

title   =  4AKE_EMcg
cpp =  /usr/bin/cpp
define  =  -DFLEXIBLE
constraints =  none
integrator  =  cg
nsteps  =  1500
nstlist =  50
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
;
;   Energy minimizing stuff
;
emtol   =  1.0
emstep  =  0.01


The minimization is successful but I don't see the meaning of this 
timestep.


Thanks,

Stefano.


Justin A. Lemkul ha scritto:



Stefano Meliga wrote:

My integrator is "steep", which should perform EM.
This is my mdp file:

title   =  4AKE_PREMsteep
cpp =  /usr/bin/cpp
define  =  -DFLEXIBLE
constraints =  all-bonds
integrator  =  steep
nsteps  =  500
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
DispCorr = no
;
;   Energy minimizing stuff
;
emtol   =  1.0
emstep  =  0.01

I learnt from the tutorials (s-peptide) that in order to do a 
position restrained MD the I have to set the constraints (all-bonds 
in this case).

Is that incorrect? Is it valid for EM as well?



Position restraints != bond contraints.  Using "constraints = 
all-bonds" will constrain the bond lengths, but not restrain the 
positions of the atoms.


If you want to do position-restrained MD, you have to "define = 
-DPOSRES" (according to the #ifdef POSRES block in the topology, 
assuming you made one automatically from pdb2gmx).  Using position 
restraints in EM doesn't serve much of a purpose in my mind, unless 
you really need to preserve the exact initial configuration; it may in 
fact prevent your system from converging if some bad geometry is being 
held in place.


-Justin


Thank you for your advice,
Stefano.


Mark Abraham ha scritto:

Stefano Meliga wrote:

Hi again,

I've tryed to perform the same preprocessing and EM steps without 
distance constraints and the situation improves a lot.
I get no warnings in the steepest descent EM and only one molecule 
cannot be set in the conjugate gradient EM.

Can you see the reason?


Yes. You're not doing EM. "t = 0.011 ps:" is a big clue. Choose your 
integrator in your .mdp file better.


Also, as Justin suggests, please be careful with the 
constraint/restraint terminology.


Mark


Thanks,
Stefano.

Stefano Meliga ha scritto:

Hi everybody,

I neutralized my system with the commands:

$grxdir/grompp -f dummy.mdp -po dummyout.mdp -c 4AKEallHsol.gro -p
4AKEallH.top -pp 4AKEallHsol_pre.top -o 4AKEallHsol.tpr
$grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb -nname
CL-
(adding the atoms to the solution SOL)

I renamed the files to keep track of the different topology files:

mv 4AKEallHsol_pre.top 4AKEallHion.top
mv "#4AKEallHsol_pre.top.1#" 4AKEallHsol_pre.top

I run an all-bonds position restraint steepest descent EM:

$grxdir/grompp -f 4AKEprePREMsteep.mdp -po 4AKE_PREMsteep.mdp -c
4AKEallHion.gro -p 4AKEallHion.top -pp 4AKEallHion_out.top -o
4AKEallHion.tpr
$grxdir/mdrun -s 4AKEallHion.tpr -o 4AKE_PREMsteep.trr -c
4AKE_PREMsteep.gro -e 4AKE_PREMsteep.edr -g 4AKE_PREMsteep.log -v

mdrun exits successfully but displays the warning:
t = 0.011 ps: Water molecule starting at atom 17223 can not be 
settled.

Check for bad contacts and/or reduce the timestep.

In the gro file atom 17223 is an oxigen of the solution

Going further with my simulation i run a all-bonds position 
restrained

conjugate gradient EM:

$grxdir/grompp -f 4AKEprePREMcg.mdp -po 4AKE_PREMcg.mdp -c
4AKE_PREMsteep.gro -p 4AKEallHion_out.top -pp 4AKEallH_PREMsteep.top
-o 4AKEallH_PREMsteep.tpr
$grxdir/mdrun -s 4AKEallH_PREMsteep.tpr -o 4AKE_PREMcg.trr -c
4AKE_PREMcg.gro -e 4AKE_PREMcg.edr -g 4AKE_PREMcg.log -v

but get the fatal error:

Source code file: constr.c, line: 136

Fatal error:
Too many LINCS warnings (2200)

And some of this warnings are again solution's mol

[gmx-users] crystals of KCl during simulation

2009-06-01 Thread Rebeca García Fandiño 

Hi,
I am trying to simulate a protein in aqueous solution 1M (KCl) with Gromacs and 
using the amber force field.

I get the topology of the solvated protein - without the ions- from amber 
(Leap) and then used the script amb2gmx.pl to obtain the Gromacs .top and .gro 
files.
I did not introduced the ions from Amber because amb2gmx.pl is only written for 
NaCl, so I used genion to ionize the system.
I added the lines correspondent to the ions in Amber to the .top of Gromacs:

[ atomtypes ]
amber99_51 K  0.  0.  A   4.73602e-01  1.37235e-03 ; K+ ion
amber99_30Cl  0.  0.  A   4.40104e-01  4.18400e-01 ; Cl- ion

[ moleculetype ]
; molname   nrexcl
K   1

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
 1  amber99_51  1K  K   1   1   39.1

[ moleculetype ]
; molname   nrexcl
Cl  1

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
 1  amber99_30  1Cl Cl  1  -1   35.45000

and everything went OK, but after equilibration I have observed that KCl is 
aggregating, like if it was making crystals. When I used NaCl instead KCl, this 
not happened.

Does anybody has any idea about the reason of the behaviour of KCl in the 
simulation?

Thank you very much in advance for your help.

Rebeca Garcia 
Academic Visitor
Dep. of Biochemistry
University of Oxford


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Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization

2009-06-01 Thread XAvier Periole 


On Jun 1, 2009, at 1:12 PM, Stefano Meliga wrote:


Hi again,

The energy minimization with conjugate gradient integrator still  
gives me two warnings of the type:


t = 0.011 ps: Water molecule starting at atom 28122 can not be  
settled.

Check for bad contacts and/or reduce the timestep.

My command lines are:

$grxdir/grompp -f 4AKEpreEMcg.mdp -po 4AKE_EMcg.mdp -c  
4AKE_EMsteep.gro -p 4AKEallHion.top -pp 4AKEpreEMsteep.top -o  
4AKE_EMcg.tpr
$grxdir/mdrun -s 4AKE_EMcg.tpr -o 4AKE_EMcg.trr -c 4AKE_EMcg.gro -e  
4AKE_EMcg.edr -g 4AKE_EMcg.log -v


This is my mdp file 4AKEpreEMcg.mdp:

title   =  4AKE_EMcg
cpp =  /usr/bin/cpp
define  =  -DFLEXIBLE
constraints =  none
integrator  =  cg
nsteps  =  1500
nstlist =  50

change that to 1

if it does not get better it means that your system is build in such a  
way that you have bad contacts
that the minimization can not remove. You have to check where there  
are and do something about it.

ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
;
;   Energy minimizing stuff
;
emtol   =  1.0
emstep  =  0.01


The minimization is successful but I don't see the meaning of this  
timestep.


Thanks,

Stefano.


Justin A. Lemkul ha scritto:



Stefano Meliga wrote:

My integrator is "steep", which should perform EM.
This is my mdp file:

title   =  4AKE_PREMsteep
cpp =  /usr/bin/cpp
define  =  -DFLEXIBLE
constraints =  all-bonds
integrator  =  steep
nsteps  =  500
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
DispCorr = no
;
;   Energy minimizing stuff
;
emtol   =  1.0
emstep  =  0.01

I learnt from the tutorials (s-peptide) that in order to do a  
position restrained MD the I have to set the constraints (all- 
bonds in this case).

Is that incorrect? Is it valid for EM as well?



Position restraints != bond contraints.  Using "constraints = all- 
bonds" will constrain the bond lengths, but not restrain the  
positions of the atoms.


If you want to do position-restrained MD, you have to "define = - 
DPOSRES" (according to the #ifdef POSRES block in the topology,  
assuming you made one automatically from pdb2gmx).  Using position  
restraints in EM doesn't serve much of a purpose in my mind, unless  
you really need to preserve the exact initial configuration; it may  
in fact prevent your system from converging if some bad geometry is  
being held in place.


-Justin


Thank you for your advice,
Stefano.


Mark Abraham ha scritto:

Stefano Meliga wrote:

Hi again,

I've tryed to perform the same preprocessing and EM steps  
without distance constraints and the situation improves a lot.
I get no warnings in the steepest descent EM and only one  
molecule cannot be set in the conjugate gradient EM.

Can you see the reason?


Yes. You're not doing EM. "t = 0.011 ps:" is a big clue. Choose  
your integrator in your .mdp file better.


Also, as Justin suggests, please be careful with the constraint/ 
restraint terminology.


Mark


Thanks,
Stefano.

Stefano Meliga ha scritto:

Hi everybody,

I neutralized my system with the commands:

$grxdir/grompp -f dummy.mdp -po dummyout.mdp -c 4AKEallHsol.gro  
-p

4AKEallH.top -pp 4AKEallHsol_pre.top -o 4AKEallHsol.tpr
$grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb - 
nname

CL-
(adding the atoms to the solution SOL)

I renamed the files to keep track of the different topology  
files:


mv 4AKEallHsol_pre.top 4AKEallHion.top
mv "#4AKEallHsol_pre.top.1#" 4AKEallHsol_pre.top

I run an all-bonds position restraint steepest descent EM:

$grxdir/grompp -f 4AKEprePREMsteep.mdp -po 4AKE_PREMsteep.mdp -c
4AKEallHion.gro -p 4AKEallHion.top -pp 4AKEallHion_out.top -o
4AKEallHion.tpr
$grxdir/mdrun -s 4AKEallHion.tpr -o 4AKE_PREMsteep.trr -c
4AKE_PREMsteep.gro -e 4AKE_PREMsteep.edr -g 4AKE_PREMsteep.log -v

mdrun exits successfully but displays the warning:
t = 0.011 ps: Water molecule starting at atom 17223 can not be  
settled.

Check for bad contacts and/or reduce the timestep.

In the gro file atom 17223 is an oxigen of the solution

Going further with my simulation i run a all-bonds position  
restrained

conjugate gradient EM:

$grxdir/grompp -f 4AKEprePREMcg.mdp -po 4AKE_PREMcg.mdp -c
4AKE_PREMsteep.gro -p 4AKEallHion_out.top -pp  
4AKEallH_PREMsteep.top

-o 4AKEallH_PREMsteep.tpr
$grxdir/mdrun -s 4AKEallH_PREMsteep.tpr -o 4AKE_PREMcg.trr -c
4AKE_PREMcg.gro -e 4AKE_PREMcg.edr -g 4AKE_PREMcg.log -v

but get the fatal error:

Source code file: constr.c, line: 136

Fatal error:
Too many LINCS warnings (2200)

And some of this warnings are again solution's molecules that  
cannot be set.
May the problem be related to the io

Re: [gmx-users] Re: solution molecules cannot be set by mdrun after neutralization

2009-06-01 Thread Stefano Meliga 

Hi again,

The energy minimization with conjugate gradient integrator still gives 
me two warnings of the type:


t = 0.011 ps: Water molecule starting at atom 28122 can not be settled.
Check for bad contacts and/or reduce the timestep.

My command lines are:

$grxdir/grompp -f 4AKEpreEMcg.mdp -po 4AKE_EMcg.mdp -c 4AKE_EMsteep.gro 
-p 4AKEallHion.top -pp 4AKEpreEMsteep.top -o 4AKE_EMcg.tpr
$grxdir/mdrun -s 4AKE_EMcg.tpr -o 4AKE_EMcg.trr -c 4AKE_EMcg.gro -e 
4AKE_EMcg.edr -g 4AKE_EMcg.log -v


This is my mdp file 4AKEpreEMcg.mdp:

title   =  4AKE_EMcg
cpp =  /usr/bin/cpp
define  =  -DFLEXIBLE
constraints =  none
integrator  =  cg
nsteps  =  1500
nstlist =  50
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
;
;   Energy minimizing stuff
;
emtol   =  1.0
emstep  =  0.01


The minimization is successful but I don't see the meaning of this timestep.

Thanks,

Stefano.


Justin A. Lemkul ha scritto:



Stefano Meliga wrote:

My integrator is "steep", which should perform EM.
This is my mdp file:

title   =  4AKE_PREMsteep
cpp =  /usr/bin/cpp
define  =  -DFLEXIBLE
constraints =  all-bonds
integrator  =  steep
nsteps  =  500
nstlist =  10
ns_type =  grid
rlist   =  1.0
rcoulomb=  1.0
rvdw=  1.0
DispCorr = no
;
;   Energy minimizing stuff
;
emtol   =  1.0
emstep  =  0.01

I learnt from the tutorials (s-peptide) that in order to do a 
position restrained MD the I have to set the constraints (all-bonds 
in this case).

Is that incorrect? Is it valid for EM as well?



Position restraints != bond contraints.  Using "constraints = 
all-bonds" will constrain the bond lengths, but not restrain the 
positions of the atoms.


If you want to do position-restrained MD, you have to "define = 
-DPOSRES" (according to the #ifdef POSRES block in the topology, 
assuming you made one automatically from pdb2gmx).  Using position 
restraints in EM doesn't serve much of a purpose in my mind, unless 
you really need to preserve the exact initial configuration; it may in 
fact prevent your system from converging if some bad geometry is being 
held in place.


-Justin


Thank you for your advice,
Stefano.


Mark Abraham ha scritto:

Stefano Meliga wrote:

Hi again,

I've tryed to perform the same preprocessing and EM steps without 
distance constraints and the situation improves a lot.
I get no warnings in the steepest descent EM and only one molecule 
cannot be set in the conjugate gradient EM.

Can you see the reason?


Yes. You're not doing EM. "t = 0.011 ps:" is a big clue. Choose your 
integrator in your .mdp file better.


Also, as Justin suggests, please be careful with the 
constraint/restraint terminology.


Mark


Thanks,
Stefano.

Stefano Meliga ha scritto:

Hi everybody,

I neutralized my system with the commands:

$grxdir/grompp -f dummy.mdp -po dummyout.mdp -c 4AKEallHsol.gro -p
4AKEallH.top -pp 4AKEallHsol_pre.top -o 4AKEallHsol.tpr
$grxdir/genion -s 4AKEallHsol.tpr -o 4AKEallHion.gro -p
4AKEallHsol_pre.top -np 4 -pname NA+ -g -pot 4AKEallHion.pdb -nname
CL-
(adding the atoms to the solution SOL)

I renamed the files to keep track of the different topology files:

mv 4AKEallHsol_pre.top 4AKEallHion.top
mv "#4AKEallHsol_pre.top.1#" 4AKEallHsol_pre.top

I run an all-bonds position restraint steepest descent EM:

$grxdir/grompp -f 4AKEprePREMsteep.mdp -po 4AKE_PREMsteep.mdp -c
4AKEallHion.gro -p 4AKEallHion.top -pp 4AKEallHion_out.top -o
4AKEallHion.tpr
$grxdir/mdrun -s 4AKEallHion.tpr -o 4AKE_PREMsteep.trr -c
4AKE_PREMsteep.gro -e 4AKE_PREMsteep.edr -g 4AKE_PREMsteep.log -v

mdrun exits successfully but displays the warning:
t = 0.011 ps: Water molecule starting at atom 17223 can not be 
settled.

Check for bad contacts and/or reduce the timestep.

In the gro file atom 17223 is an oxigen of the solution

Going further with my simulation i run a all-bonds position 
restrained

conjugate gradient EM:

$grxdir/grompp -f 4AKEprePREMcg.mdp -po 4AKE_PREMcg.mdp -c
4AKE_PREMsteep.gro -p 4AKEallHion_out.top -pp 4AKEallH_PREMsteep.top
-o 4AKEallH_PREMsteep.tpr
$grxdir/mdrun -s 4AKEallH_PREMsteep.tpr -o 4AKE_PREMcg.trr -c
4AKE_PREMcg.gro -e 4AKE_PREMcg.edr -g 4AKE_PREMcg.log -v

but get the fatal error:

Source code file: constr.c, line: 136

Fatal error:
Too many LINCS warnings (2200)

And some of this warnings are again solution's molecules that 
cannot be set.
May the problem be related to the ions added to neutralise the 
system?

mdrun was not showing this problem with the non-neutral system in
input.

Thanks a lot,
Stefano

  

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Re: [gmx-users] Re: Extend water layer along negative Z-direction

2009-06-01 Thread Tsjerk Wassenaar 
Hi Anirban,

You have to get a grip on PBC. What you're suggesting is like
extending the earth only westward, but not eastward as something is
sticking out in only one direction. It's impossible! The system is
periodic.The box vectors are direction vectors, indicating the
periodicity. Moreover, you're command to extend the box (-box 0 0
-3.5) tries to set a box with vector _lengths_ 0, 0 and -3.5. Maybe a
good idea to read Chapter 3 of the manual, regarding periodic boundary
conditions.

Cheers,

Tsjerk

On Mon, Jun 1, 2009 at 8:24 AM, Anirban Ghosh  wrote:
>
> Hi ALL,
>
> Thanks a lot Chris, Justin and Tsjerk for yor replies.
> Actually, my problem is not fully resolved. A portion of the protein tail is
> outside the water box in the Z direction (coordinate in Z is -35). So as
> suggested by you when I am issuing the command "editconf -f box.gro -o
> BOX.gro -box 0 0 -3.5", but after that genbox is giving the error:
>
> Fatal error:
> Undefined solute box.
> Create one with editconf or give explicit -box command line option
>
> Please can you specify the proper command, so that the water box is extended
> only in the negative Z direction (to solvate the portion of the protein out
> of the box)
>
> Regards,
>
>
>
>
> Anirban Ghosh
> Grade Based Engineer
> Bioinformatics Team
> Centre for Development of Advanced Computing (C-DAC)
> Pune, India
>
> 
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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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