[gmx-users] Replica Exchange MD using Gromacs

[Ruchi Gupta]

Dear gmx-users,

I am facing some problems while running replica exchange MD using Gromacs.

Few seconds after the job submission it ends with the following error message:

"
Initializing Replica Exchange
Repl  There are 6 replicas:
Multi-checking the number of atoms ... OK
Multi-checking the integrator ... OK
Multi-checking init_step+nsteps ...
init_step+nsteps is not equal for all subsystems
  subsystem 0: 0
  subsystem 1: 5
  subsystem 2: 0
  subsystem 3: 5
  subsystem 4: 0
  subsystem 5: 5

---
Program mdrun, VERSION 4.5.4
Source code file: main.c, line: 249

Fatal error:
The 6 subsystems are not compatible

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---

"

I am using a "single .gro file" and "6 different md.mdp" files (at 6
different temperatures) for generating "6 .tpr files", respectively.
But the simulation doesn't work.

I have compared the ".tpr files" using "gmxdump" and "gmxcheck"
Gromacs commands and they seem fine with respect to nsteps and
init_step information.

Does anyone have any tip over this problem?

Thanks in advance,
Ruchi Gupta.
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Re: [gmx-users] Replica Exchange MD using Gromacs

[Mark Abraham]

On 1/04/2011 6:03 PM, Ruchi Gupta wrote:

Dear gmx-users,

I am facing some problems while running replica exchange MD using Gromacs.

Few seconds after the job submission it ends with the following error message:

"
Initializing Replica Exchange

Repl  There are 6 replicas:
Multi-checking the number of atoms ... OK
Multi-checking the integrator ... OK
Multi-checking init_step+nsteps ...
init_step+nsteps is not equal for all subsystems
   subsystem 0: 0

   subsystem 1: 5
   subsystem 2: 0
   subsystem 3: 5
   subsystem 4: 0
   subsystem 5: 5

---
Program mdrun, VERSION 4.5.4
Source code file: main.c, line: 249


Fatal error:
The 6 subsystems are not compatible

For more information and tips for troubleshooting, please check the GROMACS
website athttp://www.gromacs.org/Documentation/Errors

---

"

I am using a "single .gro file" and "6 different md.mdp" files (at 6 different 
temperatures) for generating "6 .tpr files", respectively. But the simulation doesn't work.


I have compared the ".tpr files" using "gmxdump" and "gmxcheck" Gromacs 
commands and they seem fine with respect to nsteps and init_step information.


So, to be clear, gmxcheck says that for no pair of .tprs does init_step 
or nsteps differ...


What is your mdrun command line? Are you using checkpoint files?

Mark
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Re: [gmx-users] dipole moment of a charged peptide

[Dommert Florian]

On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote: 
> Hi,
>I have a long-chain peptide which has a net charge of  +5 . I was
> wondering whether the g_dipole will give any reasonable dipole moment
> for a molecule with a net charge. Is there any suggestion I should
> follow regarding calculation of dipole-moment of a charged molecule .
>  I found that in the manual it is mentioned that 'For molecules with a
> net charge, the net charge is subtracted atcenter of mass of the
> molecule.'.  I did not understand what it means. I am using
> gromacs-4.0.7.
> Sanku
> 
> 

If you have a charged molecule the dipole moment is not unique, so you
have to choose a reference point and this can be done by subtracting the
net charge at this point. Write down the formula and rearange the terms
and you will clearly see, what I mean.

Cheers,
Flo

> 
> 
> -- 
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-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658


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Re: [gmx-users] dipole moment of a charged peptide

[Erik Marklund]

Dommert Florian skrev 2011-04-01 09.45:

On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote:

Hi,
I have a long-chain peptide which has a net charge of  +5 . I was
wondering whether the g_dipole will give any reasonable dipole moment
for a molecule with a net charge. Is there any suggestion I should
follow regarding calculation of dipole-moment of a charged molecule .
  I found that in the manual it is mentioned that 'For molecules with a
net charge, the net charge is subtracted atcenter of mass of the
molecule.'.  I did not understand what it means. I am using
gromacs-4.0.7.
Sanku



If you have a charged molecule the dipole moment is not unique, so you
have to choose a reference point and this can be done by subtracting the
net charge at this point. Write down the formula and rearange the terms
and you will clearly see, what I mean.

Cheers,
Flo

And, if I recall correctly, there are two "natural" choices for this 
reference pont. One is the center of charge, the other is the center of 
mass. The latter is perhaps less intuitive, but better related to 
experimental observables.


Erik


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--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] Replica Exchange MD using Gromacs

[bsmith]

On 01/04/2011, at 6:29 PM, Mark Abraham wrote:


On 1/04/2011 6:03 PM, Ruchi Gupta wrote:

Dear gmx-users,

I am facing some problems while running replica exchange MD using  
Gromacs.


Few seconds after the job submission it ends with the following  
error message:


"
Initializing Replica Exchange

Repl  There are 6 replicas:
Multi-checking the number of atoms ... OK
Multi-checking the integrator ... OK
Multi-checking init_step+nsteps ...
init_step+nsteps is not equal for all subsystems
  subsystem 0: 0

  subsystem 1: 5
  subsystem 2: 0
  subsystem 3: 5
  subsystem 4: 0
  subsystem 5: 5

---
Program mdrun, VERSION 4.5.4
Source code file: main.c, line: 249


Fatal error:
The 6 subsystems are not compatible

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

website athttp://www.gromacs.org/Documentation/Errors

---

"

I am using a "single .gro file" and "6 different md.mdp" files (at  
6 different temperatures) for generating "6 .tpr files",  
respectively. But the simulation doesn't work.



I have compared the ".tpr files" using "gmxdump" and "gmxcheck"  
Gromacs commands and they seem fine with respect to nsteps and  
init_step information.


So, to be clear, gmxcheck says that for no pair of .tprs does  
init_step or nsteps differ...


What is your mdrun command line? Are you using checkpoint files?

Mark
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1) Comparison of the .tpr files using gmxdump reveals no differences  
but for the temperatures and the velocities in each i.e. init_step and  
nsteps have the same values (0 and 5, respectively) in all files.


2) We have tried running mdrun without checkpointing (-cpt -1) and  
with checkpointing with no change in the outcome.


Regards

Brian

Dr Brian J Smith
The Walter & Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Victoria 3052, Australia
Ph: +61 (0)3 9345 2687 Fax: +61 (0)3 9345 2686
http://www.wehi.edu.au/brian_smith





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Re: [gmx-users] dipole moment of a charged peptide

[Dommert Florian]

On Fri, 2011-04-01 at 09:48 +0200, Erik Marklund wrote: 
> Dommert Florian skrev 2011-04-01 09.45:
> > On Thu, 2011-03-31 at 18:03 -0700, Sanku M wrote:
> >> Hi,
> >> I have a long-chain peptide which has a net charge of  +5 . I was
> >> wondering whether the g_dipole will give any reasonable dipole moment
> >> for a molecule with a net charge. Is there any suggestion I should
> >> follow regarding calculation of dipole-moment of a charged molecule .
> >>   I found that in the manual it is mentioned that 'For molecules with a
> >> net charge, the net charge is subtracted atcenter of mass of the
> >> molecule.'.  I did not understand what it means. I am using
> >> gromacs-4.0.7.
> >> Sanku
> >>
> >>
> > If you have a charged molecule the dipole moment is not unique, so you
> > have to choose a reference point and this can be done by subtracting the
> > net charge at this point. Write down the formula and rearange the terms
> > and you will clearly see, what I mean.
> >
> > Cheers,
> > Flo
> >
> And, if I recall correctly, there are two "natural" choices for this 
> reference pont. One is the center of charge, the other is the center of 
> mass. The latter is perhaps less intuitive, but better related to 
> experimental observables.
> 

If you choose the center of charge as reference point, then your
molecular dipole moment will be zero, because the dipole moment for a
charged molecule can be rewritten as:

mu=qtot(x_coq-x_ref)

/Flo

> Erik
> >>
> >> -- 
> >> gmx-users mailing listgmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at 
> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-requ...@gromacs.org.
> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> 
> 


-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

Tel.: +49 - (0)711 - 68563613
Fax.: +49 - (0)711 - 68563658



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[gmx-users] FW: protein split over boundary

[anahita]

 

 

From: anahita [mailto:ana_j0...@yahoo.com] 
Sent: Friday, April 01, 2011 1:13 PM
To: 'gmx-users-requ...@gromacs.org'
Subject: protein split over boundary

 

Dear user,

Hello, I appreciate if somebody help me. During the simulation of my protein
I didn't get any error but after 1ns of MD

my molecule was split over boundary in cubic box. it means some part of it
enter the other side of the box.

At first,For decreasing the cost of simulation, in "editconf" command I set
the number "d" on 0.9  to decease the box size. I want to mention that
during the calculation my rvdw is 1.4.

I want to know instead of problem of visualization, the other things is
fine?

Best regards.

A. johari

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[gmx-users] FW: protein split over boundaries

[anahita]

 

 

From: anahita [mailto:ana_j0...@yahoo.com] 
Sent: Friday, April 01, 2011 1:13 PM
To: 'gmx-users-requ...@gromacs.org'
Subject: protein split over boundary

 

Dear user,

Hello, I appreciate if somebody help me. During the simulation of my protein
I didn't get any error but after 1ns of MD

my molecule was split over boundary in cubic box. it means some part of it
enter the other side of the box.

At first,For decreasing the cost of simulation, in "editconf" command I set
the number "d" on 0.9  to decease the box size. I want to mention that
during the calculation my rvdw is 1.4.

I want to know instead of problem of visualization, the other things is
fine?

Best regards.

A. johari

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Re: [gmx-users] Umbrella Sampling

[Gavin Melaugh]

Cheers Chris

Is the best way to check for convergence; to keep adding in more
histograms until the curves converge. Also your comment  'don't remove
any data', do you mean to keep histograms that are not so good.

Gavin
chris.ne...@utoronto.ca wrote:
> your comment:
>
> which should be centred around 0.80nm
>
> is flawed, as i mentioned earlier. also, it is not g_wham that is
> sensitive but the convergence and sampling of phase space that is
> sensitive. don`t remove any data. do evaluate your convergence.
> without convergence measures, a pmf is worse than useless.
>
> chris.
>
> -- original message --
>
> Cheers Chris
>
> If I remove the red histogram (the first of the wider distributions),
> which should be centred around 0.80nm but is actually centred around
> 0.78 nm; and add in some more histograms with higher force constants the
> profile changes slightly. It seems that  g_wham is very sensitive to
> these subtleties. How do I know which curve is correct? I have about six
> such curves that differ slightly in this manner.
>
> Gavin
>
> chris.ne...@utoronto.ca wrote:
>
> [Hide Quoted Text]
> looks fine to me, no need to do that extra sampling that I suggested
> since it appears that you already did this -- benefits of seeing real
> data ;). If you want to understand why your histograms are not always
> centered at r0 (note that this is just fine) then you should read more
> about US, WHAM, and how to bias/debias the data for US (I am sure that
> there are textbooks around that explain this). The only case in which
> all of your histograms will be centered at their respective r0 is when
> the underlying PMF is exactly flat.
>
> Chris.
>
> -- original message --
>
> Hi Chris many thanks again for the advise. I have, or at least I thought
> have sampled my barrier region to death, but as I say some histograms
> may not be centred around r0. I will proceed with what you suggest.
> Please find attached a picture of the histograms, the corresponding
> profile, and a sample mdp file that I use.
>
>

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[gmx-users] molecule split over bounderies

[ana johari]

Dear user,
Hello, I appreciate if somebody help me. During the simulation of my protein I 
didn’t get any error but after 1ns of MD
my molecule was split over boundary in cubic box. it means some part of it 
enter 
the other side of the box.
At first,For decreasing the cost of simulation, in “editconf” command I set the 
number “d” on 0.9  to decease the box size. I want to mention that during the 
calculation my rvdw is 1.4.
I want to know instead of problem of visualization, the other things is fine?
Best regards.
A. johari-- 
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Re: [gmx-users] FW: protein split over boundary

[Tsjerk Wassenaar]

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-TAW

On Fri, Apr 1, 2011 at 10:53 AM, anahita  wrote:
>
>
>
>
> From: anahita [mailto:ana_j0...@yahoo.com]
> Sent: Friday, April 01, 2011 1:13 PM
> To: 'gmx-users-requ...@gromacs.org'
> Subject: protein split over boundary
>
>
>
> Dear user,
>
> Hello, I appreciate if somebody help me. During the simulation of my protein
> I didn’t get any error but after 1ns of MD
>
> my molecule was split over boundary in cubic box. it means some part of it
> enter the other side of the box.
>
> At first,For decreasing the cost of simulation, in “editconf” command I set
> the number “d” on 0.9  to decease the box size. I want to mention that
> during the calculation my rvdw is 1.4.
>
> I want to know instead of problem of visualization, the other things is
> fine?
>
> Best regards.
>
> A. johari
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] Is there still interest in rigid-body simulation?

[mohsen ramezanpour]

Welcome :)
It is absolutely useful.

On Mon, Mar 28, 2011 at 2:32 AM, Adam Herbst  wrote:

> Hi all,
> I have seen a few posts on gmx-users indicating a desire to treat certain
> atom groups as rigid bodies in MD simulations.  I just started implementing
> this, and so far I have it working for translational forces (not rotation,
> though this should be simple to add), even when the group is split over
> multiple processors.  At the moment I have the rigid body groups specified
> as freeze groups in the mdp file, but there could be a separate option.
>  Would anyone else find this useful?  The problem is that: (a) I am
> modifying GROMACS 4.5.1, so I am some months out of date, and (b) my code is
> probably not to spec.  If it is worthwhile, I can restart from 4.5.4 (the
> code modifications are quite small) and make an effort to conform to coding
> standard.  Best,
>
> Adam Herbst
>
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Re: [gmx-users] FW: protein split over boundary

[ana johari]

Dear user,
Tanks for your attention ,I read about trjconv,but I want to know is it 
necessary  to back to the exact fram befor molecule split happens and then 
center the molecule by trjconv command?
The other point,if you attention to my value”edit conf  d=0.9 and during MD 
rvdw=1..4” is it broke the rule of periodic boundary condition or not?
tanks





From: Tsjerk Wassenaar 
To: Discussion list for GROMACS users 
Sent: Fri, April 1, 2011 1:29:19 PM
Subject: Re: [gmx-users] FW: protein split over boundary

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-TAW

On Fri, Apr 1, 2011 at 10:53 AM, anahita  wrote:
>
>
>
>
> From: anahita [mailto:ana_j0...@yahoo.com]
> Sent: Friday, April 01, 2011 1:13 PM
> To: 'gmx-users-requ...@gromacs.org'
> Subject: protein split over boundary
>
>
>
> Dear user,
>
> Hello, I appreciate if somebody help me. During the simulation of my protein
> I didn’t get any error but after 1ns of MD
>
> my molecule was split over boundary in cubic box. it means some part of it
> enter the other side of the box.
>
> At first,For decreasing the cost of simulation, in “editconf” command I set
> the number “d” on 0.9  to decease the box size. I want to mention that
> during the calculation my rvdw is 1.4.
>
> I want to know instead of problem of visualization, the other things is
> fine?
>
> Best regards.
>
> A. johari
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Re: [gmx-users] FW: protein split over boundary

[Justin A. Lemkul]

ana johari wrote:

Dear user,

Tanks for your attention ,I read about trjconv,but I want to know is it 
necessary  to back to the exact fram befor molecule split happens and 
then center the molecule by trjconv command?




If the protein starts in the center of the box, just use trjconv in conjunction 
with your original .tpr file.  A suggested trjconv workflow is on the page 
Tsjerk pointed you to.


The other point,if you attention to my value”edit conf  d=0.9 and during 
MD rvdw=1..4” is it broke the rule of periodic boundary condition or not?




In principle, no, as long as your box does not significantly deform.  Check with 
g_mindist -pi.


-Justin


tanks




*From:* Tsjerk Wassenaar 
*To:* Discussion list for GROMACS users 
*Sent:* Fri, April 1, 2011 1:29:19 PM
*Subject:* Re: [gmx-users] FW: protein split over boundary

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-TAW

On Fri, Apr 1, 2011 at 10:53 AM, anahita > wrote:

 >
 >
 >
 >
 > From: anahita [mailto:ana_j0...@yahoo.com ]
 > Sent: Friday, April 01, 2011 1:13 PM
 > To: 'gmx-users-requ...@gromacs.org 
'

 > Subject: protein split over boundary
 >
 >
 >
 > Dear user,
 >
 > Hello, I appreciate if somebody help me. During the simulation of my 
protein

 > I didn’t get any error but after 1ns of MD
 >
 > my molecule was split over boundary in cubic box. it means some part 
of it

 > enter the other side of the box.
 >
 > At first,For decreasing the cost of simulation, in “editconf” command 
I set

 > the number “d” on 0.9  to decease the box size. I want to mention that
 > during the calculation my rvdw is 1.4.
 >
 > I want to know instead of problem of visualization, the other things is
 > fine?
 >
 > Best regards.
 >
 > A. johari
 >
 > --
 > gmx-users mailing listgmx-users@gromacs.org 


 > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at
 > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to gmx-users-requ...@gromacs.org 
.

 > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 >



--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
--
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.

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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Setting the C6 LJ term for OPLSA FF

[Luca Bellucci]

Dear all
I need to change sigma and epsilon for non-bonded parameters of the OPLSA FF.
In particular I want to set the attractive part of the LJ potential to zero 
(C6=0). 
In doing this I have read the manual but unfortunately the reported 
explanation did not help me. To understand how it work in a reliable way, 
I am following the Berk suggestions available at
http://lists.gromacs.org/pipermail/gmx-users/2010-December/056303.html
and i decided to report a simple example.

The main rules are in forcefield.itp file and for OPLSA FF they are: 
 ; nbfunc   comb-rule   gen-pairs fudgeLJ fudgeQQ
 1   3  yes   0.50.5

The non-bonded force field parameters for two atoms are in ffnonbonded.itp 
file and they look like:

[ atomtypes ]
; name   bond_type  mass   charge  ptypesigma   epsilon
 opls_1   C 612.01100   0.500A   sig_1esp_1
 opls_2   O 8   15.99940   -0.500   A   sig_2eps_2

From these values I am going to define the non-bonded parameter between a 
couple of atoms as:
  
[ nonbond_params ]
  i  j func  SIG_ij  EPS_ij 
opls_1 opls_2  1(sig_1*sig2)^1/2  (eps_1*eps_2)^1/2 ; Normal behavior

However, if I want the attractive term C6 of LJ potential equal zero, I will
set sig_12=-sig_12

[ nonbond_params ]
  i  j funcSIG_ij EPS_ij 
opls_1 opls_2  1   -(sig_1*sig_2)^1/2  (eps_1*eps_2)^1/2  ; -sig_ij -> C6=0

It is right?

Thanks
 Luca

PS: because i had some problems with the gmx-users mail delivery ,i decided to 
sent this mail also to developer list.
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Re: [gmx-users] FW: protein split over boundary

[ana johari]

dear user,
Tanks for your advice,
But the mdrun is know on the step of 33562880  but the protein was split at the 
first 1ns of MD. is it necessary to use “tpbconv” command and extract the *.tpr 
file just after first 1 ns and  then use trjconv –ur compact as command.
Best regards,





From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Fri, April 1, 2011 2:52:53 PM
Subject: Re: [gmx-users] FW: protein split over boundary



ana johari wrote:
> Dear user,
> 
> Tanks for your attention ,I read about trjconv,but I want to know is it 
>necessary  to back to the exact fram befor molecule split happens and then 
>center the molecule by trjconv command?
> 

If the protein starts in the center of the box, just use trjconv in conjunction 
with your original .tpr file.  A suggested trjconv workflow is on the page 
Tsjerk pointed you to.

> The other point,if you attention to my value”edit conf  d=0.9 and during MD 
>rvdw=1..4” is it broke the rule of periodic boundary condition or not?
> 

In principle, no, as long as your box does not significantly deform.  Check 
with 
g_mindist -pi.

-Justin

> tanks
> 
> 
> 
> 
> *From:* Tsjerk Wassenaar 
> *To:* Discussion list for GROMACS users 
> *Sent:* Fri, April 1, 2011 1:29:19 PM
> *Subject:* Re: [gmx-users] FW: protein split over boundary
> 
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> 
> -TAW
> 
> On Fri, Apr 1, 2011 at 10:53 AM, anahita > wrote:
>  >
>  >
>  >
>  >
>  > From: anahita [mailto:ana_j0...@yahoo.com ]
>  > Sent: Friday, April 01, 2011 1:13 PM
>  > To: 'gmx-users-requ...@gromacs.org '
>  > Subject: protein split over boundary
>  >
>  >
>  >
>  > Dear user,
>  >
>  > Hello, I appreciate if somebody help me. During the simulation of my 
protein
>  > I didn’t get any error but after 1ns of MD
>  >
>  > my molecule was split over boundary in cubic box. it means some part of it
>  > enter the other side of the box.
>  >
>  > At first,For decreasing the cost of simulation, in “editconf” command I set
>  > the number “d” on 0.9  to decease the box size. I want to mention that
>  > during the calculation my rvdw is 1.4.
>  >
>  > I want to know instead of problem of visualization, the other things is
>  > fine?
>  >
>  > Best regards.
>  >
>  > A. johari
>  >
>  > --
>  > gmx-users mailing list    gmx-users@gromacs.org 
>
>  > http://lists.gromacs.org/mailman/listinfo/gmx-users
>  > Please search the archive at
>  > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>  > Please don't post (un)subscribe requests to the list. Use the
>  > www interface or send it to gmx-users-requ...@gromacs.org 
>.
>  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>  >
> 
> 
> 
> -- Tsjerk A. Wassenaar, Ph.D.
> 
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
> gmx-users mailing list    gmx-users@gromacs.org 
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at 
>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org 
>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] The solvent group Water is not continuous

[ahmet yıldırım]

Dear Justin,

I have Fatal Errror:The solvent group Water is not continuous. I look at
gmx-users mailing list search. I also have the same problem.
You said:(
http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)

It is exactly what I said; you've proven it. You have solvent, ligand, then
solvent. To use genion (as the program prints out at the prompt) you must have
a *continuous* group of solvent in order to embed ions. If you re-arrange the
coordinate file and [molecules] section of the topology, you can achieve this.


How can I do the re-arrange you said? Can you explain a little bit?

Thanks




-- 
Ahmet YILDIRIM
-- 
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Re: [gmx-users] Replica Exchange MD using Gromacs

[Mark Abraham]

On 1/04/2011 6:52 PM, bsmith wrote:

On 01/04/2011, at 6:29 PM, Mark Abraham wrote:


On 1/04/2011 6:03 PM, Ruchi Gupta wrote:

Dear gmx-users,

I am facing some problems while running replica exchange MD using 
Gromacs.


Few seconds after the job submission it ends with the following 
error message:


"
Initializing Replica Exchange

Repl  There are 6 replicas:
Multi-checking the number of atoms ... OK
Multi-checking the integrator ... OK
Multi-checking init_step+nsteps ...
init_step+nsteps is not equal for all subsystems
  subsystem 0: 0

  subsystem 1: 5
  subsystem 2: 0
  subsystem 3: 5
  subsystem 4: 0
  subsystem 5: 5

---
Program mdrun, VERSION 4.5.4
Source code file: main.c, line: 249


Fatal error:
The 6 subsystems are not compatible

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

website athttp://www.gromacs.org/Documentation/Errors

---

"

I am using a "single .gro file" and "6 different md.mdp" files (at 6 
different temperatures) for generating "6 .tpr files", respectively. 
But the simulation doesn't work.



I have compared the ".tpr files" using "gmxdump" and "gmxcheck" 
Gromacs commands and they seem fine with respect to nsteps and 
init_step information.


So, to be clear, gmxcheck says that for no pair of .tprs does 
init_step or nsteps differ...


What is your mdrun command line? Are you using checkpoint files?

Mark
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1) Comparison of the .tpr files using gmxdump reveals no differences 
but for the temperatures and the velocities in each i.e. init_step and 
nsteps have the same values (0 and 5, respectively) in all files.


2) We have tried running mdrun without checkpointing (-cpt -1) and 
with checkpointing with no change in the outcome.


That sounds like a bug. Please create a new Redmine issue here 
http://redmine.gromacs.org and attach your .tpr and .mdp files - 
preferably in a compressed archive file. You should get the option to 
assign it to me - please do.


Mark
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Re: [gmx-users] FW: protein split over boundary

[ravi sharma]

Hello anahita,


use pbc in your simulation.



regards,
Ravi 


  


--- On Fri, 1/4/11, anahita  wrote:

From: anahita 
Subject: [gmx-users] FW: protein split over boundary
To: "'Discussion list for GROMACS users'" 
Date: Friday, 1 April, 2011, 10:53 AM




 
 






   

   





From: anahita
[mailto:ana_j0...@yahoo.com] 

Sent: Friday, April 01, 2011 1:13 PM

To: 'gmx-users-requ...@gromacs.org'

Subject: protein split over boundary 





   

Dear user, 

Hello, I appreciate if somebody help me. During the
simulation of my protein I didn’t get any error but after 1ns of MD 

my molecule was split over boundary in cubic box. it means
some part of it enter the other side of the box. 

At first,For decreasing the cost of simulation, in
“editconf” command I set the number “d” on 0.9  to decease the box size. I
want to mention that during the calculation my rvdw is 1.4. 

I want to know instead of problem of visualization, the
other things is fine? 

Best regards. 

A. johari 



 


-Inline Attachment Follows-

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Re: [gmx-users] FW: protein split over boundary

[Justin A. Lemkul]

ana johari wrote:

dear user,

Tanks for your advice,

But the mdrun is know on the step of 33562880  but the protein was split 
at the first 1ns of MD. is  it necessary to use “tpbconv” 
command and extract the *.tpr file just after first 1 ns and  then use 
trjconv –ur compact as command.




No.  If the starting configuration had the protein properly centered in the box, 
then a simple:


trjconv -s first.tpr -f whatever_trajectory_you_want.xtc -pbc mol -center

should work to make molecules whole and center the protein in the box.

-Justin


Best regards,



*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Fri, April 1, 2011 2:52:53 PM
*Subject:* Re: [gmx-users] FW: protein split over boundary



ana johari wrote:
 > Dear user,
 >
 > Tanks for your attention ,I read about trjconv,but I want to know is 
it necessary  to back to the exact fram befor molecule split happens and 
then center the molecule by trjconv command?

 >

If the protein starts in the center of the box, just use trjconv in 
conjunction with your original .tpr file.  A suggested trjconv workflow 
is on the page Tsjerk pointed you to.


 > The other point,if you attention to my value”edit conf  d=0.9 and 
during MD rvdw=1..4” is it broke the rule of periodic boundary condition 
or not?

 >

In principle, no, as long as your box does not significantly deform.  
Check with g_mindist -pi.


-Justin

 > tanks
 >
 >
 >
 > 
 > *From:* Tsjerk Wassenaar mailto:tsje...@gmail.com>>
 > *To:* Discussion list for GROMACS users >

 > *Sent:* Fri, April 1, 2011 1:29:19 PM
 > *Subject:* Re: [gmx-users] FW: protein split over boundary
 >
 > 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

 >
 > -TAW
 >
 > On Fri, Apr 1, 2011 at 10:53 AM, anahita  >> wrote:

 >  >
 >  >
 >  >
 >  >
 >  > From: anahita [mailto:ana_j0...@yahoo.com 
 >]

 >  > Sent: Friday, April 01, 2011 1:13 PM
 >  > To: 'gmx-users-requ...@gromacs.org 
 
>'

 >  > Subject: protein split over boundary
 >  >
 >  >
 >  >
 >  > Dear user,
 >  >
 >  > Hello, I appreciate if somebody help me. During the simulation of 
my protein

 >  > I didn’t get any error but after 1ns of MD
 >  >
 >  > my molecule was split over boundary in cubic box. it means some 
part of it

 >  > enter the other side of the box.
 >  >
 >  > At first,For decreasing the cost of simulation, in “editconf” 
command I set

 >  > the number “d” on 0.9  to decease the box size. I want to mention that
 >  > during the calculation my rvdw is 1.4.
 >  >
 >  > I want to know instead of problem of visualization, the other 
things is

 >  > fine?
 >  >
 >  > Best regards.
 >  >
 >  > A. johari
 >  >
 >  > --
 >  > gmx-users mailing listgmx-users@gromacs.org 
 >

 >  > http://lists.gromacs.org/mailman/listinfo/gmx-users
 >  > Please search the archive at
 >  > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
 >  > Please don't post (un)subscribe requests to the list. Use the
 >  > www interface or send it to gmx-users-requ...@gromacs.org 
 
>.

 >  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 >  >
 >
 >
 >
 > -- Tsjerk A. Wassenaar, Ph.D.
 >
 > post-doctoral researcher
 > Molecular Dynamics Group
 > * Groningen Institute for Biomolecular Research and Biotechnology
 > * Zernike Institute for Advanced Materials
 > University of Groningen
 > The Netherlands
 > --
 > gmx-users mailing listgmx-users@gromacs.org 
 >

 > http://lists.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!

 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to gmx-users-requ...@gromacs.org 
 
>.

 > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
 >

-- 

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

===

Re: [gmx-users] The solvent group Water is not continuous

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear Justin,

I have Fatal Errror:The solvent group Water is not continuous. I look at 
gmx-users mailing list search. I also have the same problem.
You 
said:(http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)


It is exactly what I said; you've proven it. You have solvent, ligand, then
solvent. To use genion (as the program prints out at the prompt) you must have
a *continuous* group of solvent in order to embed ions. If you re-arrange the

coordinate file and [molecules] section of the topology, you can achieve this.


How can I do the re-arrange you said? Can you explain a little bit?



I don't know what there is to explain.  Water must be continuous in both the 
coordinate file and the topology in order to use genion.  You haven't said 
what's in your system or what you've done to it up to this point.


-Justin


Thanks




--
Ahmet YILDIRIM



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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Re: [gmx-users] The solvent group Water is not continuous

[Mark Abraham]

On 1/04/2011 10:26 PM, ahmet yıldırım wrote:

Dear Justin,

I have Fatal Errror:The solvent group Water is not continuous. I look 
at gmx-users mailing list search. I also have the same problem.
You 
said:(http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)

It is exactly what I said; you've proven it. You have solvent, ligand, then
solvent. To use genion (as the program prints out at the prompt) you must have
a *continuous* group of solvent in order to embed ions. If you re-arrange the

coordinate file and [molecules] section of the topology, you can achieve this.

How can I do the re-arrange you said? Can you explain a little bit?


You need a system topology whose molecules are ordered such that all the 
water is contiguous. That means the order of the names of molecule types 
in your [ molecules ] section of your .top can have only one mention of 
water. Since the order of molecules in the coordinate file must match 
this order, you will need to physically reorder your [ molecules ] 
section, and the chunks of molecules in your coordinate file. 
Fortunately, you don't have to renumber those atoms in the coordinate file.


Mark
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Re: [gmx-users] The solvent group Water is not continuous

[ahmet yıldırım]

Dear Dr. Mark,

I did you said but I have the same error. please look at attached file

topol.top:

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
SOL   185
SOL   143
SOL 44125
TRS1
EDO1



01 Nisan 2011 14:41 tarihinde Mark Abraham  yazdı:

> On 1/04/2011 10:26 PM, ahmet yıldırım wrote:
>
>> Dear Justin,
>>
>> I have Fatal Errror:The solvent group Water is not continuous. I look at
>> gmx-users mailing list search. I also have the same problem.
>> You said:(
>> http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)
>> It is exactly what I said; you've proven it. You have solvent, ligand,
>> then
>> solvent. To use genion (as the program prints out at the prompt) you must
>> have
>> a *continuous* group of solvent in order to embed ions. If you re-arrange
>> the
>>
>> coordinate file and [molecules] section of the topology, you can achieve
>> this.
>>
>> How can I do the re-arrange you said? Can you explain a little bit?
>>
>
> You need a system topology whose molecules are ordered such that all the
> water is contiguous. That means the order of the names of molecule types in
> your [ molecules ] section of your .top can have only one mention of water.
> Since the order of molecules in the coordinate file must match this order,
> you will need to physically reorder your [ molecules ] section, and the
> chunks of molecules in your coordinate file. Fortunately, you don't have to
> renumber those atoms in the coordinate file.
>
> 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/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Ahmet YILDIRIM


topol.top
Description: Binary data
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Re: [gmx-users] The solvent group Water is not continuous

[Mark Abraham]

On 1/04/2011 11:03 PM, ahmet yıldırım wrote:

Dear Dr. Mark,

I did you said but I have the same error. please look at attached file

topol.top:

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
SOL   185
SOL   143
SOL 44125
TRS1
EDO1


OK, well maybe it doesn't like different chunks of the same molecule 
even when they're adjacent in order. Try "SOL 44453" instead.


Mark

01 Nisan 2011 14:41 tarihinde Mark Abraham > yazdı:


On 1/04/2011 10:26 PM, ahmet yıldırım wrote:

Dear Justin,

I have Fatal Errror:The solvent group Water is not continuous.
I look at gmx-users mailing list search. I also have the same
problem.
You

said:(http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)
It is exactly what I said; you've proven it. You have solvent,
ligand, then
solvent. To use genion (as the program prints out at the
prompt) you must have
a *continuous* group of solvent in order to embed ions. If you
re-arrange the

coordinate file and [molecules] section of the topology, you
can achieve this.

How can I do the re-arrange you said? Can you explain a little
bit?


You need a system topology whose molecules are ordered such that
all the water is contiguous. That means the order of the names of
molecule types in your [ molecules ] section of your .top can have
only one mention of water. Since the order of molecules in the
coordinate file must match this order, you will need to physically
reorder your [ molecules ] section, and the chunks of molecules in
your coordinate file. Fortunately, you don't have to renumber
those atoms in the coordinate file.

Mark

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Re: [gmx-users] The solvent group Water is not continuous

[ahmet yıldırım]

I tried SOL 44453 but I still the same error

01 Nisan 2011 15:11 tarihinde Mark Abraham  yazdı:

>  On 1/04/2011 11:03 PM, ahmet yıldırım wrote:
>
> Dear Dr. Mark,
>
> I did you said but I have the same error. please look at attached file
>
> topol.top:
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_A 1
> Protein_chain_B 1
> SOL   185
> SOL   143
> SOL 44125
> TRS1
> EDO1
>
>
> OK, well maybe it doesn't like different chunks of the same molecule even
> when they're adjacent in order. Try "SOL 44453" instead.
>
> Mark
>
>
>  01 Nisan 2011 14:41 tarihinde Mark Abraham yazdı:
>
>>  On 1/04/2011 10:26 PM, ahmet yıldırım wrote:
>>
>>> Dear Justin,
>>>
>>> I have Fatal Errror:The solvent group Water is not continuous. I look at
>>> gmx-users mailing list search. I also have the same problem.
>>> You said:(
>>> http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)
>>> It is exactly what I said; you've proven it. You have solvent, ligand,
>>> then
>>> solvent. To use genion (as the program prints out at the prompt) you must
>>> have
>>> a *continuous* group of solvent in order to embed ions. If you re-arrange
>>> the
>>>
>>> coordinate file and [molecules] section of the topology, you can achieve
>>> this.
>>>
>>> How can I do the re-arrange you said? Can you explain a little bit?
>>>
>>
>>  You need a system topology whose molecules are ordered such that all the
>> water is contiguous. That means the order of the names of molecule types in
>> your [ molecules ] section of your .top can have only one mention of water.
>> Since the order of molecules in the coordinate file must match this order,
>> you will need to physically reorder your [ molecules ] section, and the
>> chunks of molecules in your coordinate file. Fortunately, you don't have to
>> renumber those atoms in the coordinate file.
>>
>> 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/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Ahmet YILDIRIM
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>



-- 
Ahmet YILDIRIM
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Re: [gmx-users] The solvent group Water is not continuous

[Erik Marklund]

Is it a problem with an index file? is 'Water' an index group, and if 
so, is is contiguous.


Erik

ahmet yıldırım skrev 2011-04-01 14.15:

I tried SOL 44453 but I still the same error

01 Nisan 2011 15:11 tarihinde Mark Abraham > yazdı:


On 1/04/2011 11:03 PM, ahmet yıldırım wrote:

Dear Dr. Mark,

I did you said but I have the same error. please look at attached
file

topol.top:

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
SOL   185
SOL   143
SOL 44125
TRS1
EDO1


OK, well maybe it doesn't like different chunks of the same
molecule even when they're adjacent in order. Try "SOL 44453" instead.

Mark



01 Nisan 2011 14:41 tarihinde Mark Abraham
mailto:mark.abra...@anu.edu.au>> yazdı:

On 1/04/2011 10:26 PM, ahmet yıldırım wrote:

Dear Justin,

I have Fatal Errror:The solvent group Water is not
continuous. I look at gmx-users mailing list search. I
also have the same problem.
You

said:(http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)
It is exactly what I said; you've proven it. You have
solvent, ligand, then
solvent. To use genion (as the program prints out at the
prompt) you must have
a *continuous* group of solvent in order to embed ions.
If you re-arrange the

coordinate file and [molecules] section of the topology,
you can achieve this.

How can I do the re-arrange you said? Can you explain a
little bit?


You need a system topology whose molecules are ordered such
that all the water is contiguous. That means the order of the
names of molecule types in your [ molecules ] section of your
.top can have only one mention of water. Since the order of
molecules in the coordinate file must match this order, you
will need to physically reorder your [ molecules ] section,
and the chunks of molecules in your coordinate file.
Fortunately, you don't have to renumber those atoms in the
coordinate file.

Mark

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--
Ahmet YILDIRIM



--
---
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 4537fax: +46 18 511 755
er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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Re: [gmx-users] The solvent group Water is not continuous

[Justin A. Lemkul]

ahmet yıldırım wrote:

I tried SOL 44453 but I still the same error



Are you using some index file that is specifying a discontinuous water group? 
Have you properly re-created your genion input .tpr file from this new topology?


-Justin

01 Nisan 2011 15:11 tarihinde Mark Abraham > yazdı:


On 1/04/2011 11:03 PM, ahmet yıldırım wrote:

Dear Dr. Mark,

I did you said but I have the same error. please look at attached file

topol.top:

[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
SOL   185
SOL   143
SOL 44125
TRS1
EDO1


OK, well maybe it doesn't like different chunks of the same molecule
even when they're adjacent in order. Try "SOL 44453" instead.

Mark



01 Nisan 2011 14:41 tarihinde Mark Abraham
mailto:mark.abra...@anu.edu.au>> yazdı:

On 1/04/2011 10:26 PM, ahmet yıldırım wrote:

Dear Justin,

I have Fatal Errror:The solvent group Water is not
continuous. I look at gmx-users mailing list search. I
also have the same problem.
You

said:(http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)
It is exactly what I said; you've proven it. You have
solvent, ligand, then
solvent. To use genion (as the program prints out at the
prompt) you must have
a *continuous* group of solvent in order to embed ions. If
you re-arrange the

coordinate file and [molecules] section of the topology,
you can achieve this.

How can I do the re-arrange you said? Can you explain a
little bit?


You need a system topology whose molecules are ordered such
that all the water is contiguous. That means the order of the
names of molecule types in your [ molecules ] section of your
.top can have only one mention of water. Since the order of
molecules in the coordinate file must match this order, you
will need to physically reorder your [ molecules ] section,
and the chunks of molecules in your coordinate file.
Fortunately, you don't have to renumber those atoms in the
coordinate file.

Mark

-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before
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-- 
Ahmet YILDIRIM



--
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Please search the archive at
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--
Ahmet YILDIRIM



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] The solvent group Water is not continuous

[ahmet yıldırım]

Dear users,

I created nonaminoacid TRS.itp and EDO.itp files using ProDrg Beta.

genion -s em.tpr -o solvated.gro -nname Na -nn 15 -g em.log
select group:13
Fatal error:
The solvent group SOL is not continuous: index[984]=5334, index[985]=5355
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



01 Nisan 2011 15:17 tarihinde Justin A. Lemkul  yazdı:

>
>
> ahmet yıldırım wrote:
>
>> I tried SOL 44453 but I still the same error
>>
>>
> Are you using some index file that is specifying a discontinuous water
> group? Have you properly re-created your genion input .tpr file from this
> new topology?
>
> -Justin
>
>  01 Nisan 2011 15:11 tarihinde Mark Abraham > mark.abra...@anu.edu.au>> yazdı:
>>
>>
>>On 1/04/2011 11:03 PM, ahmet yıldırım wrote:
>>
>>>Dear Dr. Mark,
>>>
>>>I did you said but I have the same error. please look at attached file
>>>
>>>topol.top:
>>>
>>>[ molecules ]
>>>; Compound#mols
>>>Protein_chain_A 1
>>>Protein_chain_B 1
>>>SOL   185
>>>SOL   143
>>>SOL 44125
>>>TRS1
>>>EDO1
>>>
>>
>>OK, well maybe it doesn't like different chunks of the same molecule
>>even when they're adjacent in order. Try "SOL 44453" instead.
>>
>>Mark
>>
>>
>> 01 Nisan 2011 14:41 tarihinde Mark Abraham
>>>mailto:mark.abra...@anu.edu.au>> yazdı:
>>>
>>>
>>>On 1/04/2011 10:26 PM, ahmet yıldırım wrote:
>>>
>>>Dear Justin,
>>>
>>>I have Fatal Errror:The solvent group Water is not
>>>continuous. I look at gmx-users mailing list search. I
>>>also have the same problem.
>>>You
>>>said:(
>>> http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)
>>>It is exactly what I said; you've proven it. You have
>>>solvent, ligand, then
>>>solvent. To use genion (as the program prints out at the
>>>prompt) you must have
>>>a *continuous* group of solvent in order to embed ions. If
>>>you re-arrange the
>>>
>>>coordinate file and [molecules] section of the topology,
>>>you can achieve this.
>>>
>>>How can I do the re-arrange you said? Can you explain a
>>>little bit?
>>>
>>>
>>>You need a system topology whose molecules are ordered such
>>>that all the water is contiguous. That means the order of the
>>>names of molecule types in your [ molecules ] section of your
>>>.top can have only one mention of water. Since the order of
>>>molecules in the coordinate file must match this order, you
>>>will need to physically reorder your [ molecules ] section,
>>>and the chunks of molecules in your coordinate file.
>>>Fortunately, you don't have to renumber those atoms in the
>>>coordinate file.
>>>
>>>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/Support/Mailing_Lists/Search before
>>>posting!
>>>Please don't post (un)subscribe requests to the list. Use the
>>>www interface or send it to gmx-users-requ...@gromacs.org
>>>.
>>>
>>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>>>
>>>-- Ahmet YILDIRIM
>>>
>>
>>
>>--
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>
>>http://lists.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at
>>http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to gmx-users-requ...@gromacs.org
>>.
>>
>>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>> --
>> Ahmet YILDIRIM
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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>



-- 
Ahmet YILDIR

Re: [gmx-users] The solvent group Water is not continuous

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear users,

I created nonaminoacid TRS.itp and EDO.itp files using ProDrg Beta.



...and hopefully did a complete re-parameterization of the nonsense charges it 
gives.


http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

That's an aside, completely unrelated to your actual problem, though.


genion -s em.tpr -o solvated.gro -nname Na -nn 15 -g em.log
select group:13
Fatal error:
The solvent group SOL is not continuous: index[984]=5334, index[985]=5355
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors



You still haven't answered the second question I posed below.  I assume this 
"em.tpr" file has not been re-generated from a properly continuous .gro and .top 
combination.  If either were out of order with respect to the other (i.e. 
changing the .top and not the .gro), you would have gotten a fatal error from 
grompp when creating em.tpr.


-Justin




01 Nisan 2011 15:17 tarihinde Justin A. Lemkul > yazdı:




ahmet yıldırım wrote:

I tried SOL 44453 but I still the same error


Are you using some index file that is specifying a discontinuous
water group? Have you properly re-created your genion input .tpr
file from this new topology?

-Justin

01 Nisan 2011 15:11 tarihinde Mark Abraham
mailto:mark.abra...@anu.edu.au>
>> yazdı:


   On 1/04/2011 11:03 PM, ahmet yıldırım wrote:

   Dear Dr. Mark,

   I did you said but I have the same error. please look at
attached file

   topol.top:

   [ molecules ]
   ; Compound#mols
   Protein_chain_A 1
   Protein_chain_B 1
   SOL   185
   SOL   143
   SOL 44125
   TRS1
   EDO1


   OK, well maybe it doesn't like different chunks of the same
molecule
   even when they're adjacent in order. Try "SOL 44453" instead.

   Mark


   01 Nisan 2011 14:41 tarihinde Mark Abraham
   mailto:mark.abra...@anu.edu.au>
>> yazdı:


   On 1/04/2011 10:26 PM, ahmet yıldırım wrote:

   Dear Justin,

   I have Fatal Errror:The solvent group Water is not
   continuous. I look at gmx-users mailing list
search. I
   also have the same problem.
   You
 
 said:(http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)

   It is exactly what I said; you've proven it. You have
   solvent, ligand, then
   solvent. To use genion (as the program prints out
at the
   prompt) you must have
   a *continuous* group of solvent in order to embed
ions. If
   you re-arrange the

   coordinate file and [molecules] section of the
topology,
   you can achieve this.

   How can I do the re-arrange you said? Can you
explain a
   little bit?


   You need a system topology whose molecules are
ordered such
   that all the water is contiguous. That means the
order of the
   names of molecule types in your [ molecules ] section
of your
   .top can have only one mention of water. Since the
order of
   molecules in the coordinate file must match this
order, you
   will need to physically reorder your [ molecules ]
section,
   and the chunks of molecules in your coordinate file.
   Fortunately, you don't have to renumber those atoms
in the
   coordinate file.

   Mark

   -- gmx-users mailing list  
 gmx-users@gromacs.org 

   >

   http://lists.gromacs.org/mailman/listinfo/gmx-users
   Please search the archive at
   http://www.gromacs.org/Support/Mailing_Lists/Search
before
   posting!
   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] The solvent group Water is not continuous

[ahmet yıldırım]

When I created em.tpr I got the followings notes:
*NOTE 1 [file topol.top, line 52]:*
  System has non-zero total charge: -1.50e+01

*NOTE 2 [file topol.top]:*
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

then, I tried to add ions.

Thanks

01 Nisan 2011 15:33 tarihinde Justin A. Lemkul  yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>>
>> I created nonaminoacid TRS.itp and EDO.itp files using ProDrg Beta.
>>
>>
> ...and hopefully did a complete re-parameterization of the nonsense charges
> it gives.
>
> http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
>
> That's an aside, completely unrelated to your actual problem, though.
>
>
>  genion -s em.tpr -o solvated.gro -nname Na -nn 15 -g em.log
>> select group:13
>> Fatal error:
>> The solvent group SOL is not continuous: index[984]=5334, index[985]=5355
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
> You still haven't answered the second question I posed below.  I assume
> this "em.tpr" file has not been re-generated from a properly continuous .gro
> and .top combination.  If either were out of order with respect to the other
> (i.e. changing the .top and not the .gro), you would have gotten a fatal
> error from grompp when creating em.tpr.
>
> -Justin
>
>
>>
>> 01 Nisan 2011 15:17 tarihinde Justin A. Lemkul > jalem...@vt.edu>> yazdı:
>>
>>
>>
>>
>>ahmet yıldırım wrote:
>>
>>I tried SOL 44453 but I still the same error
>>
>>
>>Are you using some index file that is specifying a discontinuous
>>water group? Have you properly re-created your genion input .tpr
>>file from this new topology?
>>
>>-Justin
>>
>>01 Nisan 2011 15:11 tarihinde Mark Abraham
>>mailto:mark.abra...@anu.edu.au>
>>>>> yazdı:
>>
>>
>>   On 1/04/2011 11:03 PM, ahmet yıldırım wrote:
>>
>>   Dear Dr. Mark,
>>
>>   I did you said but I have the same error. please look at
>>attached file
>>
>>   topol.top:
>>
>>   [ molecules ]
>>   ; Compound#mols
>>   Protein_chain_A 1
>>   Protein_chain_B 1
>>   SOL   185
>>   SOL   143
>>   SOL 44125
>>   TRS1
>>   EDO1
>>
>>
>>   OK, well maybe it doesn't like different chunks of the same
>>molecule
>>   even when they're adjacent in order. Try "SOL 44453" instead.
>>
>>   Mark
>>
>>
>>   01 Nisan 2011 14:41 tarihinde Mark Abraham
>>   mailto:mark.abra...@anu.edu.au>
>>>>> yazdı:
>>
>>
>>   On 1/04/2011 10:26 PM, ahmet yıldırım wrote:
>>
>>   Dear Justin,
>>
>>   I have Fatal Errror:The solvent group Water is not
>>   continuous. I look at gmx-users mailing list
>>search. I
>>   also have the same problem.
>>   You
>>  said:(
>> http://lists.gromacs.org/pipermail/gmx-users/2010-January/048344.html)
>>   It is exactly what I said; you've proven it. You
>> have
>>   solvent, ligand, then
>>   solvent. To use genion (as the program prints out
>>at the
>>   prompt) you must have
>>   a *continuous* group of solvent in order to embed
>>ions. If
>>   you re-arrange the
>>
>>   coordinate file and [molecules] section of the
>>topology,
>>   you can achieve this.
>>
>>   How can I do the re-arrange you said? Can you
>>explain a
>>   little bit?
>>
>>
>>   You need a system topology whose molecules are
>>ordered such
>>   that all the water is contiguous. That means the
>>order of the
>>   names of molecule types in your [ molecules ] section
>>of your
>>   .top can have only one mention of water. Since the
>>order of
>>   molecules in the coordinate file must match this
>>order, you
>>   will need to physically reorder your [ molecules ]
>>  

Re: [gmx-users] The solvent group Water is not continuous

[Justin A. Lemkul]

ahmet yıldırım wrote:

When I created em.tpr I got the followings notes:
*_NOTE 1 [file topol.top, line 52]:_*
  System has non-zero total charge: -1.50e+01
 
_*NOTE 2 [file topol.top]:*_

  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

then, I tried to add ions.



Neither of these notes is relevant to the problem at hand, although the second 
means that some component of your topology is badly broken.


Just to be very clear, after rearranging your .gro and .top such that (1) they 
match and (2) all solvent molecules are continuous, you have created a new .tpr 
file and you're still getting an error from genion?


-Justin


Thanks

01 Nisan 2011 15:33 tarihinde Justin A. Lemkul > yazdı:




ahmet yıldırım wrote:

Dear users,

I created nonaminoacid TRS.itp and EDO.itp files using ProDrg Beta.


...and hopefully did a complete re-parameterization of the nonsense
charges it gives.

http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

That's an aside, completely unrelated to your actual problem, though.


genion -s em.tpr -o solvated.gro -nname Na -nn 15 -g em.log
select group:13
Fatal error:
The solvent group SOL is not continuous: index[984]=5334,
index[985]=5355
For more information and tips for troubleshooting, please check
the GROMACS
website at http://www.gromacs.org/Documentation/Errors


You still haven't answered the second question I posed below.  I
assume this "em.tpr" file has not been re-generated from a properly
continuous .gro and .top combination.  If either were out of order
with respect to the other (i.e. changing the .top and not the .gro),
you would have gotten a fatal error from grompp when creating em.tpr.

-Justin



01 Nisan 2011 15:17 tarihinde Justin A. Lemkul mailto:jalem...@vt.edu> >> yazdı:




   ahmet yıldırım wrote:

   I tried SOL 44453 but I still the same error


   Are you using some index file that is specifying a discontinuous
   water group? Have you properly re-created your genion input .tpr
   file from this new topology?

   -Justin

   01 Nisan 2011 15:11 tarihinde Mark Abraham
   mailto:mark.abra...@anu.edu.au>
>
   
    >
   
   

[gmx-users] Umbrella Sampling

[chris . neale]

1. how do you know that data is "not good"? It is not good science to  
remove data just because it doesn't match with your expected results.  
For now, there is no compelling reason to remove that data.


2. My first step in checking the convergence is to block average the  
time. If you have 10 ns total per umbrella, then extract the first 0-1  
ns  and make a PMF based on that. Then extract the 1-2 ns data and  
make a PMF based on that. Continue until you make a PMF based on the  
9-10 ns data. Now check and see if this PMF is drifting over time. You  
can do this by looking at the PMFs or by integrating the bound state  
and plotting the binding free energy as a function of equilibration  
time. If the binding free energy is still drifiting as a function of  
increasing equilibration time then you are certainly unconverged. Note  
that there will always be noise in this measure, but what you are  
looking for is unidirectional drift in the value. -- One could write a  
textbook on this topic. i suggest that you seek out alternative  
resources to understand how to check convergence properly.


Chris.


Cheers Chris

Is the best way to check for convergence; to keep adding in more
histograms until the curves converge. Also your comment  'don't remove
any data', do you mean to keep histograms that are not so good.

Gavin
chris.neale at utoronto.ca wrote:

your comment:

which should be centred around 0.80nm

is flawed, as i mentioned earlier. also, it is not g_wham that is
sensitive but the convergence and sampling of phase space that is
sensitive. don`t remove any data. do evaluate your convergence.
without convergence measures, a pmf is worse than useless.

chris.

-- original message --

Cheers Chris

If I remove the red histogram (the first of the wider distributions),
which should be centred around 0.80nm but is actually centred around
0.78 nm; and add in some more histograms with higher force constants the
profile changes slightly. It seems that  g_wham is very sensitive to
these subtleties. How do I know which curve is correct? I have about six
such curves that differ slightly in this manner.

Gavin

chris.neale at utoronto.ca wrote:

[Hide Quoted Text]
looks fine to me, no need to do that extra sampling that I suggested
since it appears that you already did this -- benefits of seeing real
data ;). If you want to understand why your histograms are not always
centered at r0 (note that this is just fine) then you should read more
about US, WHAM, and how to bias/debias the data for US (I am sure that
there are textbooks around that explain this). The only case in which
all of your histograms will be centered at their respective r0 is when
the underlying PMF is exactly flat.

Chris.

-- original message --

Hi Chris many thanks again for the advise. I have, or at least I thought
have sampled my barrier region to death, but as I say some histograms
may not be centred around r0. I will proceed with what you suggest.
Please find attached a picture of the histograms, the corresponding
profile, and a sample mdp file that I use.



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[gmx-users] R: Re: adding a new residue in the ff

[Anna Marabotti]

Dear Justin and Tsjerk,
thank you very much for your last encouraging words...;-) I don't remember a
time in my life where something that I needed, which was very complex to do,
was already available...(apart from Gromacs package, of course!)
About parameterization: sure I was intended to use the parameters for Cys
residue as much as possible. I was thinking of adding all angles, bonds,
dihedrals etc until the CB, and using the topology created by PRODRG only
for SO3 moiety. If I understand well, Tsjerk suggests not to include the
CA-CB-SG angle. Concerning charges, I was planning to calculate them using
Antechamber, following Justin's suggestions about the problems of Prodrg.
IIRC, apart from charges, bonds, angles, dihedrals etc. obtained with Prodrg
were substantially correct, so I was thinking of adding directly these
values to my ffbonded.itp. The atom types of SO3 seem to be already present
in the ffG43a1, since they are identified as SDSMO and OM. Do you think that
with these data I would be able to add the bonds, angles etc to my
ffbonded.itp, to aminoacids.rtp and all other files I have to modify in the
ffG43a1 local forcefield? I don't think to be able to obtain an "exact"
parameterization, but I hope it would be at least acceptable...
Many thanks 
Anna


--

Message: 1
Date: Thu, 31 Mar 2011 19:27:17 +0200
From: Tsjerk Wassenaar 
Subject: Re: [gmx-users] adding a new residue in the ff
To: jalem...@vt.edu, Discussion list for GROMACS users

Message-ID:

Content-Type: text/plain; charset=ISO-8859-1

Hi,

> It would probably be easier, faster, and more accurate to just use most of
> the parameters for Cys rather than try to have PRODRG re-create a
> (potentially flawed) model of your compound.  The only new parameters are
> related to SO3, so the rest should be identical to the Cys residue.

That's not a good idea. It'll only do for the backbone. The charge of
CB will be quite different, as well as the CA-CB-SG angle, and for the
rest there's nothing similar even.

> This is where parameterization becomes a chore - when there's nothing
> analogous to what you're doing.  Proper Gromos96 parameterization
> methodology would dictate that you generate an analogous compound (i.e.,
> methyl sulfonic acid) and adjust its parameters such that it reproduces
> various condensed-phase thermodynamic and physical properties (DeltaG of
> solvation, liquid density, heat of vaporization).  Proper derivation is
> quite time-consuming.  Perhaps someone has already done this work and it
is
> published.  If you're unlucky, you've got to do it all yourself.

That's a good idea :)

Cheers,

Tsjerk



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands


--

Message: 2
Date: Thu, 31 Mar 2011 13:29:54 -0400
From: "Justin A. Lemkul" 
Subject: Re: [gmx-users] adding a new residue in the ff
To: "Gromacs Users' List" 
Message-ID: <4d94ba12.5030...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed



Tsjerk Wassenaar wrote:
> Hi,
> 
>> It would probably be easier, faster, and more accurate to just use most
of
>> the parameters for Cys rather than try to have PRODRG re-create a
>> (potentially flawed) model of your compound.  The only new parameters are
>> related to SO3, so the rest should be identical to the Cys residue.
> 
> That's not a good idea. It'll only do for the backbone. The charge of
> CB will be quite different, as well as the CA-CB-SG angle, and for the
> rest there's nothing similar even.
> 

Gah, that's what I meant.  Thanks for pointing that out!  I guess I've
stated so 
many times (and published on the fact) that PRODRG charges are useless that
I'm 
no longer even quoting myself...

-Justin

>> This is where parameterization becomes a chore - when there's nothing
>> analogous to what you're doing.  Proper Gromos96 parameterization
>> methodology would dictate that you generate an analogous compound (i.e.,
>> methyl sulfonic acid) and adjust its parameters such that it reproduces
>> various condensed-phase thermodynamic and physical properties (DeltaG of
>> solvation, liquid density, heat of vaporization).  Proper derivation is
>> quite time-consuming.  Perhaps someone has already done this work and it
is
>> published.  If you're unlucky, you've got to do it all yourself.
> 
> That's a good idea :)
> 
> Cheers,
> 
> Tsjerk
> 
> 
> 

-- 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin





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http://lists.

Re: [gmx-users] R: Re: adding a new residue in the ff

[Justin A. Lemkul]

Anna Marabotti wrote:

Dear Justin and Tsjerk,
thank you very much for your last encouraging words...;-) I don't remember a
time in my life where something that I needed, which was very complex to do,
was already available...(apart from Gromacs package, of course!)
About parameterization: sure I was intended to use the parameters for Cys
residue as much as possible. I was thinking of adding all angles, bonds,
dihedrals etc until the CB, and using the topology created by PRODRG only
for SO3 moiety. If I understand well, Tsjerk suggests not to include the
CA-CB-SG angle. Concerning charges, I was planning to calculate them using
Antechamber, following Justin's suggestions about the problems of Prodrg.


Results from Antechamber directly are probably not sufficient as an end state 
for parameterization.  See our recent paper about this: 
http://pubs.acs.org/doi/abs/10.1021/ci100335w.  Antechamber gives you a 
reasonable starting point, but the calculations do not even replicate the most 
trivial species in the Gromos96 43A1 parameter set (nor would you necessarily 
expect them to).



IIRC, apart from charges, bonds, angles, dihedrals etc. obtained with Prodrg
were substantially correct, so I was thinking of adding directly these
values to my ffbonded.itp. The atom types of SO3 seem to be already present


If they're "correct," then what do you need to add?  If they are already part of 
the parent force field (i.e., PRODRG chose correct values) then you do not need 
to re-define existing parameters (and in fact, grompp may raise a fatal error if 
you do).



in the ffG43a1, since they are identified as SDSMO and OM. Do you think that
with these data I would be able to add the bonds, angles etc to my
ffbonded.itp, to aminoacids.rtp and all other files I have to modify in the
ffG43a1 local forcefield? I don't think to be able to obtain an "exact"
parameterization, but I hope it would be at least acceptable...


Your desired level of accuracy is up to you, but most careful reviewers do not 
consider partial efforts to be sufficient.  Close enough is not necessarily good 
enough.  The approximations or substitutions you make need to be justifiable, 
which I guess is about as good as anyone can recommend.


-Justin

Many thanks 
Anna



--

Message: 1
Date: Thu, 31 Mar 2011 19:27:17 +0200
From: Tsjerk Wassenaar 
Subject: Re: [gmx-users] adding a new residue in the ff
To: jalem...@vt.edu, Discussion list for GROMACS users

Message-ID:

Content-Type: text/plain; charset=ISO-8859-1

Hi,


It would probably be easier, faster, and more accurate to just use most of
the parameters for Cys rather than try to have PRODRG re-create a
(potentially flawed) model of your compound.  The only new parameters are
related to SO3, so the rest should be identical to the Cys residue.


That's not a good idea. It'll only do for the backbone. The charge of
CB will be quite different, as well as the CA-CB-SG angle, and for the
rest there's nothing similar even.


This is where parameterization becomes a chore - when there's nothing
analogous to what you're doing.  Proper Gromos96 parameterization
methodology would dictate that you generate an analogous compound (i.e.,
methyl sulfonic acid) and adjust its parameters such that it reproduces
various condensed-phase thermodynamic and physical properties (DeltaG of
solvation, liquid density, heat of vaporization).  Proper derivation is
quite time-consuming.  Perhaps someone has already done this work and it

is

published.  If you're unlucky, you've got to do it all yourself.


That's a good idea :)

Cheers,

Tsjerk





--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] tpr file for trjconv command

[ana johari]

Dear user,
During simulation I restart the Md run and know I have two .tpr file. Because 
my 
molecule split over boundary after 1 ns of simulation,I want to use “trjconv” 
as 
a command to center my molecule but I don’t know to chose my first tpr file( 
for 
the first 1ns) or the second one after restarting.
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[gmx-users] (no subject)

[ana johari]

Dear Justin,Tsjerkand and Ravi,
thanks from all of you for your kindness,
I hop that I could use your recommend.
anahita johari-- 
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Re: [gmx-users] tpr file for trjconv command

[Justin A. Lemkul]

ana johari wrote:

Dear user,

During simulation I restart the Md run and know I have two .tpr file. 
Because my molecule split over boundary after 1 ns of simulation,I want 
to use “trjconv” as a command to center my molecule but I don’t know to 
chose my first tpr file( for the first 1ns) or the second one after 
restarting.


Use the first one, which I've said at least twice now.  Think about what you're 
trying to achieve - some sort of fitting to a reference structure such that the 
protein stays in some convenient (but ultimately, arbitrary) location.


If you start with a protein properly centered within the box (at time zero, i.e. 
the state in the first .tpr file), then that's a sensible reference, is it not? 
 It is possible to fit to whatever reference you wish, any intermediate frame 
or other .tpr file, but if you're not comfortable with these concepts yet, do 
what is most intuitive and fit to your starting state.  Doing so will produce a 
smooth trajectory that you can visualize very easily.


-Justin



Tanks

 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] OPLS parametrizaton

[Marcelo Silva]

Hi,

I am trying to simulate mixtures of ethanol and trifluoroethanol and I 
would like to use the same parameters used on OPLS parametrization.


On the OPLS1996 paper the authors starts by stating that they've used 
267 molecules and "The box size varied from approximately 26 26  26 Å 
for methanol to 37  37  37 Å for cyclohexane". In my simulations I am 
considering using 500 molecules (each box vector would be around 37 Å).


"In most cases, the intermolecular nonbonded interactions were truncated 
at 11Å based on roughly the center-of-mass separations with quadratic 
smoothing of the interaction energy to zero over the last 0.5 Å (...) A 
standard correction was made for the Lennard-Jones interactions 
neglected beyond the cutoff."


Trying to interpret what is written I think the correct way to treat 
cut-offs and energy corrections would be like this:


---
Cut-offs

rlist= 1.4
coulombtype  = Reaction-field-zero
rcoulomb = 1.1
rcuolomb_shift  = 0.6
vdwtype   = shift
rvdw = 1.1
rvdw_switch= 0.6

Dispersion Correction

DispCorr = EnerPress

---

However I have some doubts because I'm using a box with a different 
number of molecules/ different size (should I change the cutoffs to 15Å 
like it was for cyclohexane?) and I'm not sure about using 
Reaction-field-zero instead of the shift function for coulombic 
interactions.


Could you please help me confirm this parameters so I can run a 
simulation in the same conditions as OPLS was parameterized (although 
using MC and not MD).


Best regards,

Marcelo
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[gmx-users] distance restraints for atoms on 2 chains

[Sai Pooja]

Hi,

I have 5 chains in my Protein. I want to apply distance restraints for doing
Umbrella Sampling for 2 atoms on different chains. Is there a way to do this
since the two chains have separater itp files.

Pooja

-- 
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[gmx-users] Re: distance restraints for atoms on 2 chains

[Sai Pooja]

Also, the chains do not diffuse apart in time since they are position
restrained(some parts of each chain are ...)

On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja  wrote:

> Hi,
>
> I have 5 chains in my Protein. I want to apply distance restraints for
> doing Umbrella Sampling for 2 atoms on different chains. Is there a way to
> do this since the two chains have separater itp files.
>
> Pooja
>
> --
> Quaerendo Invenietis-Seek and you shall discover.
>



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Re: [gmx-users] Re: distance restraints for atoms on 2 chains

[Justin A. Lemkul]

pdb2gmx -chainsep (-merge in 4.0.x and before) should allow you to create a 
merged [moleculetype] to apply distance restraints.  If you're just trying to 
use a harmonic potential to define some sampling distance (for US), then 
distance restraints are not necessary, just apply the pull code.


-Justin

Sai Pooja wrote:
Also, the chains do not diffuse apart in time since they are position 
restrained(some parts of each chain are ...)


On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja > wrote:


Hi,
 
I have 5 chains in my Protein. I want to apply distance restraints

for doing Umbrella Sampling for 2 atoms on different chains. Is
there a way to do this since the two chains have separater itp files.
 
Pooja


-- 
Quaerendo Invenietis-Seek and you shall discover.





--
Quaerendo Invenietis-Seek and you shall discover.



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] OPLS parametrizaton

[Justin A. Lemkul]

Marcelo Silva wrote:

Hi,

I am trying to simulate mixtures of ethanol and trifluoroethanol and I 
would like to use the same parameters used on OPLS parametrization.


On the OPLS1996 paper the authors starts by stating that they've used 
267 molecules and "The box size varied from approximately 26 26  26 Å 
for methanol to 37  37  37 Å for cyclohexane". In my simulations I am 
considering using 500 molecules (each box vector would be around 37 Å).


"In most cases, the intermolecular nonbonded interactions were truncated 
at 11Å based on roughly the center-of-mass separations with quadratic 
smoothing of the interaction energy to zero over the last 0.5 Å (...) A 
standard correction was made for the Lennard-Jones interactions 
neglected beyond the cutoff."


Trying to interpret what is written I think the correct way to treat 
cut-offs and energy corrections would be like this:


---
Cut-offs

rlist= 1.4
coulombtype  = Reaction-field-zero
rcoulomb = 1.1
rcuolomb_shift  = 0.6
vdwtype   = shift
rvdw = 1.1
rvdw_switch= 0.6

Dispersion Correction

DispCorr = EnerPress

---

However I have some doubts because I'm using a box with a different 
number of molecules/ different size (should I change the cutoffs to 15Å 
like it was for cyclohexane?) and I'm not sure about using 
Reaction-field-zero instead of the shift function for coulombic 
interactions.


Could you please help me confirm this parameters so I can run a 
simulation in the same conditions as OPLS was parameterized (although 
using MC and not MD).




I don't think there is a perfectly clear answer to this.  OPLS was initially 
designed for MC with some special functional forms and is now applied to MD 
using all manner of settings.  Commonly, one sees rcoulomb=rvdw=rlist=1.0 or 1.4 
in conjunction with PME.  There have been a variety of systematic force field 
comparisons in recent years.  You should consult those to see what their 
specific recommendations are with respect to proper settings, although many of 
them focus on proteins.


-Justin


Best regards,

Marcelo


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Re: distance restraints for atoms on 2 chains

[Sai Pooja]

The pull tutorial uses npt simulations.. is that required by the algorithm
or can one use nvt after the system has been sufficiently equilibrated using
npt?

On Fri, Apr 1, 2011 at 7:32 PM, Justin A. Lemkul  wrote:

>
> pdb2gmx -chainsep (-merge in 4.0.x and before) should allow you to create a
> merged [moleculetype] to apply distance restraints.  If you're just trying
> to use a harmonic potential to define some sampling distance (for US), then
> distance restraints are not necessary, just apply the pull code.
>
> -Justin
>
> Sai Pooja wrote:
>
>> Also, the chains do not diffuse apart in time since they are position
>> restrained(some parts of each chain are ...)
>>
>> On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja > saipo...@gmail.com>> wrote:
>>
>>Hi,
>> I have 5 chains in my Protein. I want to apply distance restraints
>>for doing Umbrella Sampling for 2 atoms on different chains. Is
>>there a way to do this since the two chains have separater itp files.
>> Pooja
>>
>>-- Quaerendo Invenietis-Seek and you shall discover.
>>
>>
>>
>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
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>



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Re: [gmx-users] Re: distance restraints for atoms on 2 chains

[Justin A. Lemkul]

Sai Pooja wrote:
The pull tutorial uses npt simulations.. is that required by the 
algorithm or can one use nvt after the system has been sufficiently 
equilibrated using npt?




Use whatever conditions are appropriate for your system.  Tutorials should not 
be viewed as the only applicable conditions, merely one such example of what 
might be done.


-Justin

On Fri, Apr 1, 2011 at 7:32 PM, Justin A. Lemkul > wrote:



pdb2gmx -chainsep (-merge in 4.0.x and before) should allow you to
create a merged [moleculetype] to apply distance restraints.  If
you're just trying to use a harmonic potential to define some
sampling distance (for US), then distance restraints are not
necessary, just apply the pull code.

-Justin

Sai Pooja wrote:

Also, the chains do not diffuse apart in time since they are
position restrained(some parts of each chain are ...)

On Fri, Apr 1, 2011 at 7:26 PM, Sai Pooja mailto:saipo...@gmail.com> >> wrote:

   Hi,
I have 5 chains in my Protein. I want to apply distance
restraints
   for doing Umbrella Sampling for 2 atoms on different chains. Is
   there a way to do this since the two chains have separater
itp files.
Pooja

   -- Quaerendo Invenietis-Seek and you shall discover.




-- 
Quaerendo Invenietis-Seek and you shall discover.



-- 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu  | (540) 231-9080

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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--
Quaerendo Invenietis-Seek and you shall discover.


--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Precision mismatch

[Sai Pooja]

Hi

Precision mismatch for state entry nosehoover-xi, code precision is double,
file precision is float

I am trying to extend an mdrun from a restart file. I get the error pasted
above. The restart file was generated on a different cluster and I am now
extending these simulations. Can this be resolved?

Pooja

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Re: [gmx-users] Precision mismatch

[Justin A. Lemkul]

Sai Pooja wrote:

Hi
 
Precision mismatch for state entry nosehoover-xi, code precision is 
double, file precision is float
 
I am trying to extend an mdrun from a restart file. I get the error 
pasted above. The restart file was generated on a different cluster and 
I am now extending these simulations. Can this be resolved?
 


Install Gromacs with matching precision.

-Justin


Pooja

--
Quaerendo Invenietis-Seek and you shall discover.



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Precision mismatch

[Mark Abraham]

On 02/04/11, Sai Pooja   wrote:
> Hi
> 
>  
> 
> Precision mismatch for state entry nosehoover-xi, code precision is double, 
> file precision is float
> 
>  
> 
> I am trying to extend an mdrun from a restart file. I get the error pasted 
> above. The restart file was generated on a different cluster and I am now 
> extending these simulations. Can this be resolved?
> 
> 

Sure. Use a single-precision version of GROMACS on the new cluster (and tell 
the admins that the double-precision version of GROMACS has a different 
executable suffix for a reason...).

Mark
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