Re: [gmx-users] xtc corrupted during REMD

[andrea spitaleri]

Hi,
two on five have magic error at the same time. The simulation ends fine. Just the xtc files are 
corrupted. The magic error is systematic, since I repeated the simulation 4 times and I get the same 
behavior (at different time) after the continuing run. First time, I suspected for some I/O error, 
but now it sounds a bit strange. I will ask for a long simulation 50ns without extending steps.


thanks in advance

regards

and


On 11/22/2010 05:44 AM, Roland Schulz wrote:



On Sun, Nov 21, 2010 at 2:05 PM, Spitaleri Andrea
mailto:spitaleri.and...@hsr.it>> wrote:

Hi,
yes sure. Basically I do:

1. mdrun -s runA_ -deffnm runA_ -replex 5000 -multi 5 -> i get the
first 5x25ns of remd simulation (five xtc every 5ps and five trr
every 20ps, for each replica). I check those files by gmxcheck and
they are fine. no errors.

2. for i in 'seq 1 5'; tpbconv -s runA_$i -nsteps 2500 -o
runB_$i -> extension the simulation to 50ns total

3. mdrun -s runB_ -replex 5000 -multi 5 -deffnm runB_ -cpi runA_  ->
at end some (2 or 1 on the 5 xtc file) of the xtc are corrupted
(from gmxcheck) whereas the trr are fine. These are from 25ns to 50ns.

 >From the log file I do not see any errors. Everything seems fine.
I have free room space in the hd too :)

I am just wondering whether the problem is in the xtc options
(precision and writing step)


I doubt it that it has anything to do with your xtc options.

Are all you xtc corrupted or only some? Are those which are corrupted
all corrupted on the same frame or different ones?

Roland



Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStatistics
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://sites.google.com/site/andreaspitaleri/
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153


Da: gmx-users-boun...@gromacs.org

[gmx-users-boun...@gromacs.org
] per conto di Mark Abraham
[mark.abra...@anu.edu.au ]
Inviato: domenica 21 novembre 2010 17.03
A: Discussion list for GROMACS users
Oggetto: Re: [gmx-users] xtc corrupted during REMD

On 21/11/2010 2:34 AM, Spitaleri Andrea wrote:
 > Hi there,
 > I am encountering a weird problem with a REMD simulation using
4.5.3. The total simulation is 50ns with 5 replica, and I do in two
runs: 25ns and then continuing to 50ns (walltime queue). The first
run is okay, the continue run (the last 25ns) randomly make some xtc
files corrupted (from gmxcheck I get the Magic Number Error).

I don't understand how the simulation can continue writing the .xtc
files when you are getting magic number errors from gmxcheck. We need to
see command lines for your workflow, please :-)

Mark

 >   It is strange since the respective trr files are okay and the
simulation is still going (it is not blowing up from the log, not
step.pdb files, not crash). The only difference is that I am writing
the xtc often respect to the trr file and just the complex not the
solvent:
 >
 > nstxout = 1 ; coordinates every 20ps
 > nstvout = 0 ; velocity every 0ps
 > nstfout = 0 ; forces every 0 ps
 > nstlog  = 2500 ; energies log every 5ps
 > nstenergy   = 2500 ; energies  every 5ps
 > nstxtcout   = 2500 ; coordinates every 5ps to xtc
 > xtc-precision   = 2500 ;
 > xtc-grps= complex;
 >
 >
 > Since the error is happening only for the continuing run, I am
just wondering if there is any reason for this.
 >
 > thanks for any help
 >
 >
 > and
 >
 > 
 > Andrea Spitaleri PhD
 > Dulbecco Telethon Institute
 > Center of Genomics, BioInformatics and BioStatistics
 > c/o DIBIT Scientific Institute
 > Biomolecular NMR, 1B4
 > Via Olgettina 58
 > 20132 Milano (Italy)
 > http://sites.google.com/site/andreaspitaleri/
 > Tel: 0039-0226434348/5622/3497/4922
 > Fax: 0039-0226434153
 > 
 >
 >
 >

---
 > SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE.
 > NON C'E' CURA SENZA RICERCA.
 > Per donazioni: ccp 42437681 intestato a Fondazione Arete' Onlus
del San Raffaele.
 > Per informazioni: tel. 02.2643.4461 - www.sanraffaele.org


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Re: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

[Erik Marklund]

Jignesh Patel skrev 2010-11-22 08.57:

Dear all,

Can anybody tell me how to incorporate potassium ion parameters in 
GROMACS for GROMOS53a6 forcefield.


Thanking you in anticipation.

With regards,
Jignesh



If you have decent parameters, add them to ions.itp

--
---
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er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/

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RE: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

[#ZHAO LINA#]

I just tried the same way as using NA+, by

 genion -s ions.tpr -o protein_solvated_ions.gro -p topol.top -pname K+ -nname 
CL- -np Number_of_K

It works, u may do a try.

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Jignesh Patel [jbp...@gmail.com]
Sent: Monday, November 22, 2010 3:57 PM
To: gromacs user
Subject: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

Dear all,

Can anybody tell me how to incorporate potassium ion parameters in GROMACS for 
GROMOS53a6 forcefield.

Thanking you in anticipation.

With regards,
Jignesh


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RE: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

[#ZHAO LINA#]

When I went a bit further, I found it's wrong.

Sorry.

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of #ZHAO LINA# [zhao0...@e.ntu.edu.sg]
Sent: Monday, November 22, 2010 4:50 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

I just tried the same way as using NA+, by

 genion -s ions.tpr -o protein_solvated_ions.gro -p topol.top -pname K+ -nname 
CL- -np Number_of_K

It works, u may do a try.

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Jignesh Patel [jbp...@gmail.com]
Sent: Monday, November 22, 2010 3:57 PM
To: gromacs user
Subject: [gmx-users] potassium ion incorporation in GROMOS53a6 forcefield

Dear all,

Can anybody tell me how to incorporate potassium ion parameters in GROMACS for 
GROMOS53a6 forcefield.

Thanking you in anticipation.

With regards,
Jignesh


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RE: [gmx-users] mdrun -rerun: bonded interactions of protein

[NG HUI WEN]

Dear Mark and Justin,

 

I have a potentially silly question here. I have been trying to work out
the figures from the various options of g_energy. You mentioned before
that the bonded terms are not decomposable/require some hacking with the
.top file. I am a bit confused with that.

 

As mentioned previously, I did 

1)grompp -f new.mdp -n index.ndx -c old.tpr -o rerun1.tpr -p topol.top

Where energy groups are added to the .mdp file

 

2)tpbconv -s rerun1.tpr -n index -o rerun2.tpr -nsteps 0 

To produce individual .tpr files for i) System  ii) Protein only  iii)
Lipid only  iv) solv_ion only  v) protein_lipid  vi) protein_solv_ion
vii) lipid_solv_ion

 

3)trjconv  -f old.trr  -n index.ndx  -s rerun2.tpr  -o rerun.trr

To produce a corresponding .trr files for (i) to (vii) in step 2

 

4) mdrun -s rerun2.tpr  -rerun  rerun.trr

To produce the .edr files for (i) to (vii)

 

With g_energy I derived these different components for (i) to (vii):

a-PE

b-Angle (lipid)/G96 angle (protein)

c-Proper dihedral

d-Improper dihedral

e-Ryckaert Belleman (lipid)

f-LJ 1-4

g-Coul 1-4

h-L J SR

i-Disp. Corr

j-Coul SR

k-Coul. Recip

 

After doing some maths, I got the below:

1)  the PEs for (i) to (vii) are the sum of their corresponding b-k
values

e.g. the PE for the system =  Angle (lipid) + G96 angle (protein) +
Prop. Dihedral + imp dihedral + Ryckaert Belleman (lipid) + LJ14 + Coul
1-4 + LJ SR + Disp Corr + Coul SR + Coul recip. 

2)  For bonded terms such as proper dihedral, I found that the
proper dihedral of the system (i) = (ii) + (iii) i.e sum of proper
dihedral values from protein and lipid. The same goes for the improper
dihedral term. This is where I am confused. Doesn't this show that the
bonded terms can be decomposed?

 

I realize there has been a rather long pause between this email and the
last, sorry about that, it's because I have been trying to work out
myself why you say the bonded terms cannot be decomposed easily.

 

Perhaps as Justin pointed out, it is probably not worth the effort to
derive individual energies of the various components that make up my
system, but I would really appreciate a reply on this before I put the
matter to rest. Thanks!

 

HW

 

 

From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham
Sent: Friday, November 12, 2010 12:32 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] mdrun -rerun: bonded interactions of protein

 

On 11/11/2010 7:46 PM, NG HUI WEN wrote: 

Thanks a lot Justin and Mark for your useful input.

 

Indeed Justin was right, the quest to dissect the total energy of the
system to get that contributed by the protein alone was not trivial at
all! 


Indeed. If I'd observed you were doing PME, I'd have made the same
point. 




I missed out this thread yesterday
http://www.mail-archive.com/gmx-users@gromacs.org/msg34610.html as well
as Mark's trick to decompose bonded terms by hacking the .top file.
(However, I read from
http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy that the
Coul-recip term is not decomposable regardless of the tricks used...)

 

Mark, following your advice, I added -nsteps 0 (-1 didn't work) to
tpbconv. I managed to get the interactive prompt succesfully this time. 


Yes, nsteps=-1 is a GROMACS 4.5-ism, sorry. 




Reading toplogy and shit from rerun1.tpr
Reading file rerun1.tpr, VERSION 4.0.7 (single precision)
Setting nsteps to 0
Group 0 (  System) has 100581 elements
Group 1 ( Protein) has  4002 elements
Group 2 (   Protein-H) has  3145 elements
Group 3 ( C-alpha) has   412 elements
Group 4 (Backbone) has  1236 elements
Group 5 (   MainChain) has  1649 elements
Group 6 (MainChain+Cb) has  2027 elements
Group 7 ( MainChain+H) has  2039 elements
Group 8 (   SideChain) has  1963 elements
Group 9 ( SideChain-H) has  1496 elements
Group10 ( Prot-Masses) has  4002 elements
Group11 ( Non-Protein) has 96579 elements
Group12 (POPE) has 13052 elements
Group13 ( SOL) has 83523 elements
Group14 ( CL-) has 4 elements
Group15 (   Other) has 96579 elements
Group16 ( SOL_CL-) has 83527 elements
Group17 (Protein_POPE) has 17054 elements
Select a group: 

 

As suggested, I have also tried to compare the (average) values of
subset.tpr and fullsystem.tpr, these are the total energies of:

System=  -1.28209 e+06

Protein=  -9571.86

Lipid=-296121

SOL_CL=  -821353

Other= -1.22684e+06

It was found that the: 

Total energies (Protein + lipid + SOL_CL-) not equal to total energy of
the system

Total energies of (Lipid + SOL_CL-) not equal to total energy of other

Total energies of (others + protein) not equal to total energy of the
system

 

I have yet to work out the reasons for the discrepancies, will spend
some time pondering and trying to make sense of t

[gmx-users] protein folding

[mohsen ramezanpour]

Dear All

I am searching for a tutorial for  learning how to do protein folding with
Gromacs.
Do any one know such tutorials?
Please let me know them.

Thanks in advance
Sincerely
Mohsen
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[gmx-users] .pqr to .pdb

[mohsen ramezanpour]

Dear  All

I had a pdb file who was incomplete,there were not  some atom coordinates in
the file.
I used a server  who repaired it for me.
The result was a .pqr file .

Do you know any simple way for  transforming  .pqr file to .pdb?
I want to see the structure with Pymol and it can't read pqr format.

Thanks in advance
Best
Mohsen
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Re: [gmx-users] .pqr to .pdb

[Mark Abraham]

On 22/11/2010 10:16 PM, mohsen ramezanpour wrote:

Dear  All

I had a pdb file who was incomplete,there were not  some atom 
coordinates in the file.

I used a server  who repaired it for me.
The result was a .pqr file .

Do you know any simple way for  transforming  .pqr file to .pdb?
I want to see the structure with Pymol and it can't read pqr format.


Ask it for a pdb format. There should be no tool that builds atoms that 
cannot write a standard file format like PDB - particularly as PQR is a 
derivative of PDB.


Oh, and this is a bit off-topic for this list :-)

Mark
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Re: [gmx-users] protein folding

[Mark Abraham]

On 22/11/2010 10:09 PM, mohsen ramezanpour wrote:

Dear All

I am searching for a tutorial for  learning how to do protein folding 
with Gromacs.

Do any one know such tutorials?
Please let me know them.


There aren't any, because basically no proteins fold on the time scales 
that are accessible to GROMACS molecular dynamics simulations.


Google will certainly be your friend when searching for GROMACS 
tutorials, however.


Mark
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Re: [gmx-users] protein folding

[ms]

On 22/11/10 11:09, mohsen ramezanpour wrote:

Dear All

I am searching for a tutorial for  learning how to do protein folding with
Gromacs.
Do any one know such tutorials?
Please let me know them.


I don't think so because managing to fold a protein in a MD simulation 
is no easy task. In theory, if you have a lot of patience and a lot of 
computational resources, it's no different from a normal MD simulation, 
but good luck even getting *close* to a folded state.


So, it all depends on what you want really to know, and in this case 
several techniques may help you (REMD, metadynamics, etc.) but I think 
you have to read a lot of literature to make up your mind on such stuff.


M.


Thanks in advance
Sincerely
Mohsen





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[gmx-users] grompp error version 4.5.2

[Adva Suez]

Hello,
I'm using your KALP in DPPC tutorial to figure out how to simulate a
molecule in a membrane in GROMACS. I'm using version 4.5.2 and from some
reason I got an error in grompp whe trying generate md_0_1.tpr.
the error is:

Program grompp_mpi, VERSION 4.5.2
Source code file: enxio.c, line: 1097

Fatal error:
Could not find frame with time 1000.61 in
'../../membed_17_npt.edr.884814.edr'

This is weird because I only have 1000 frames in the NPT run...
Can you please help me?

Thanks,
Adva.


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 G.S.W. Faculty of Life Sciences
 Tel-Aviv University, ISRAEL 69978

 Tel: 972-3-6406840; Fax: 972-3-6405098
 E-mail: sueza...@tauex.tau.ac.il
 Web-site:
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Re: [gmx-users] grompp error version 4.5.2

[Mark Abraham]

On 22/11/2010 11:03 PM, Adva Suez wrote:

Hello,
I'm using your KALP in DPPC tutorial to figure out how to simulate a  
molecule in a membrane in GROMACS. I'm using version 4.5.2 and from 
some reason I got an error in grompp whe trying generate md_0_1.tpr.

the error is:

Program grompp_mpi, VERSION 4.5.2
Source code file: enxio.c, line: 1097

Fatal error:
Could not find frame with time 1000.61 in 
'../../membed_17_npt.edr.884814.edr'


That's a seriously weird .edr file name. What was your command line?

Mark


This is weird because I only have 1000 frames in the NPT run...
Can you please help me?

Thanks,
Adva.


--
Adva Yeheskel
Bioinformatics Unit
Rm 001, Sherman bldg.,
 G.S.W. Faculty of Life Sciences
 Tel-Aviv University, ISRAEL 69978

 Tel: 972-3-6406840; Fax: 972-3-6405098
 E-mail: sueza...@tauex.tau.ac.il 
 Web-site:
http://www.tau.ac.il/lifesci/bioinformatics.html 





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Re: [gmx-users] xtc corrupted during REMD

[Mark Abraham]

On 22/11/2010 7:11 PM, andrea spitaleri wrote:

Hi,
two on five have magic error at the same time. The simulation ends 
fine. Just the xtc files are corrupted. The magic error is systematic, 
since I repeated the simulation 4 times and I get the same behavior 
(at different time) after the continuing run. First time, I suspected 
for some I/O error, but now it sounds a bit strange. I will ask for a 
long simulation 50ns without extending steps.


Hmm. A GROMACS code problem is most likely to be manifest by exactly 
reproducible behaviour. A filesystem problem would be erratic, but 
should not only occur on run extensions. You could try the continuations 
with mdrun -reprod to eliminate a few GROMACS-related 
non-reproducibility attributes. This is more of a diagnostic than a 
long-term solution, however.


Mark

thanks in advance

regards

and


On 11/22/2010 05:44 AM, Roland Schulz wrote:



On Sun, Nov 21, 2010 at 2:05 PM, Spitaleri Andrea
mailto:spitaleri.and...@hsr.it>> wrote:

Hi,
yes sure. Basically I do:

1. mdrun -s runA_ -deffnm runA_ -replex 5000 -multi 5 -> i get the
first 5x25ns of remd simulation (five xtc every 5ps and five trr
every 20ps, for each replica). I check those files by gmxcheck and
they are fine. no errors.

2. for i in 'seq 1 5'; tpbconv -s runA_$i -nsteps 2500 -o
runB_$i -> extension the simulation to 50ns total

3. mdrun -s runB_ -replex 5000 -multi 5 -deffnm runB_ -cpi runA_  ->
at end some (2 or 1 on the 5 xtc file) of the xtc are corrupted
(from gmxcheck) whereas the trr are fine. These are from 25ns to 
50ns.


>From the log file I do not see any errors. Everything seems fine.
I have free room space in the hd too :)

I am just wondering whether the problem is in the xtc options
(precision and writing step)


I doubt it that it has anything to do with your xtc options.

Are all you xtc corrupted or only some? Are those which are corrupted
all corrupted on the same frame or different ones?

Roland



Andrea Spitaleri PhD
Dulbecco Telethon Institute
Center of Genomics, BioInformatics and BioStatistics
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://sites.google.com/site/andreaspitaleri/
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153


Da: gmx-users-boun...@gromacs.org

[gmx-users-boun...@gromacs.org
] per conto di Mark Abraham
[mark.abra...@anu.edu.au ]
Inviato: domenica 21 novembre 2010 17.03
A: Discussion list for GROMACS users
Oggetto: Re: [gmx-users] xtc corrupted during REMD

On 21/11/2010 2:34 AM, Spitaleri Andrea wrote:
> Hi there,
> I am encountering a weird problem with a REMD simulation using
4.5.3. The total simulation is 50ns with 5 replica, and I do in two
runs: 25ns and then continuing to 50ns (walltime queue). The first
run is okay, the continue run (the last 25ns) randomly make some xtc
files corrupted (from gmxcheck I get the Magic Number Error).

I don't understand how the simulation can continue writing the .xtc
files when you are getting magic number errors from gmxcheck. We 
need to

see command lines for your workflow, please :-)

Mark

>   It is strange since the respective trr files are okay and the
simulation is still going (it is not blowing up from the log, not
step.pdb files, not crash). The only difference is that I am writing
the xtc often respect to the trr file and just the complex not the
solvent:
>
> nstxout = 1 ; coordinates every 20ps
> nstvout = 0 ; velocity every 0ps
> nstfout = 0 ; forces every 0 ps
> nstlog  = 2500 ; energies log every 5ps
> nstenergy   = 2500 ; energies  every 5ps
> nstxtcout   = 2500 ; coordinates every 5ps to xtc
> xtc-precision   = 2500 ;
> xtc-grps= complex;
>
>
> Since the error is happening only for the continuing run, I am
just wondering if there is any reason for this.
>
> thanks for any help
>
>
> and
>
> 
> Andrea Spitaleri PhD
> Dulbecco Telethon Institute
> Center of Genomics, BioInformatics and BioStatistics
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
> http://sites.google.com/site/andreaspitaleri/
> Tel: 0039-0226434348/5622/3497/4922
> Fax: 0039-0226434153
> 
>
>
>

---

> SOSTIENI ANCHE TU LA RICERCA DEL SAN RAFFAELE.
> NON C'E' CURA SENZA RICERCA.
> Per do

Re: [gmx-users] protein folding

[Thomas Evangelidis]

With respect to protein folding, I want to fold a 42 amino acid loop (part
of a protein domain with known structure) which has no homologous
counterpart in PDB. Ab initio servers fail to assign a compact tertiary
structure to the loop, so I would like to see how MD tools can cope with
this problem. I 'm wondering if there is any way to keep the rest of the
protein rigid while running the simulation, cause the loop interacts with
the protein surface at many points.Is simulated annealing the right
approach? I'd appreciate any advice as I think the time scale of the problem
I described is accessible to MD.

thanks in advance,
Thomas



On 22 November 2010 13:48, ms  wrote:

> On 22/11/10 11:09, mohsen ramezanpour wrote:
>
>> Dear All
>>
>> I am searching for a tutorial for  learning how to do protein folding with
>> Gromacs.
>> Do any one know such tutorials?
>> Please let me know them.
>>
>
> I don't think so because managing to fold a protein in a MD simulation is
> no easy task. In theory, if you have a lot of patience and a lot of
> computational resources, it's no different from a normal MD simulation, but
> good luck even getting *close* to a folded state.
>
> So, it all depends on what you want really to know, and in this case
> several techniques may help you (REMD, metadynamics, etc.) but I think you
> have to read a lot of literature to make up your mind on such stuff.
>
>
> M.
>
>  Thanks in advance
>> Sincerely
>> Mohsen
>>
>>
>>
>
> --
> Massimo Sandal, Ph.D.
> http://devicerandom.org
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] How to obtain the coordinates of atom 100 with number in the frame 100 using xdrfile in C code

[英雄不再寂寞]

Dear gmxers,
   I do not know whether this question is suitable here. If not, please just 
neglect it. However, this question puzzles me greatly, that is, how to obtain 
the coordinates of atom 100 with number in the frame 100 using xdrfile in C 
code. Here 100 is only an example for some defined atom or frame. In my 
opinions, the xdrfile lib is quite valuable tool to use for the custom analysis 
using C code. Unfortunately, there are no documents about how to use it 
effectively. Could you please give me some hints to do so? Thanks a lot for any 
reply.
 Yours sincerely,
 Chaofu Wu, Dr.-- 
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Re: [gmx-users] protein folding

[David van der Spoel]

On 2010-11-22 13.27, Thomas Evangelidis wrote:

With respect to protein folding, I want to fold a 42 amino acid loop
(part of a protein domain with known structure) which has no homologous
counterpart in PDB. Ab initio servers fail to assign a compact tertiary
structure to the loop, so I would like to see how MD tools can cope with
this problem. I 'm wondering if there is any way to keep the rest of the
protein rigid while running the simulation, cause the loop interacts
with the protein surface at many points.Is simulated annealing the right
approach? I'd appreciate any advice as I think the time scale of the
problem I described is accessible to MD.

I would go for REMD with position restraints on the C-alpha's of the 
part of the protein for which you know the structure. To speed it up, 
you might want to try loop prediction servers to get different starting 
structures, however 42 is a long loop. Note that you will have to do 
quite a long REMD > 100 ns I would think.

thanks in advance,
Thomas



On 22 November 2010 13:48, ms mailto:deviceran...@gmail.com>> wrote:

On 22/11/10 11:09, mohsen ramezanpour wrote:

Dear All

I am searching for a tutorial for  learning how to do protein
folding with
Gromacs.
Do any one know such tutorials?
Please let me know them.


I don't think so because managing to fold a protein in a MD
simulation is no easy task. In theory, if you have a lot of patience
and a lot of computational resources, it's no different from a
normal MD simulation, but good luck even getting *close* to a folded
state.

So, it all depends on what you want really to know, and in this case
several techniques may help you (REMD, metadynamics, etc.) but I
think you have to read a lot of literature to make up your mind on
such stuff.


M.

Thanks in advance
Sincerely
Mohsen




--
Massimo Sandal, Ph.D.
http://devicerandom.org

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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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Re: [gmx-users] How to obtain the coordinates of atom 100 with number in the frame 100 using xdrfile in C code

[David van der Spoel]

On 2010-11-22 13.36,  wrote:

Dear gmxers,
I do not know whether this question is suitable here. If not, please
just neglect it. However, this question puzzles me greatly, that is, how
to obtain the coordinates of atom 100 with number in the frame 100 using
xdrfile in C code. Here 100 is only an example for some defined atom or
frame. In my opinions, the xdrfile lib is quite valuable tool to use for
the custom analysis using C code. Unfortunately, there are no documents
about how to use it effectively. Could you please give me some hints to
do so? Thanks a lot for any reply.
Yours sincerely,
Chaofu Wu, Dr.

You just have to read a whole frame and extract the coordinate that you 
want.


--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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RE: [gmx-users] mdrun -rerun: bonded interactions of protein

[Justin A. Lemkul]

Quoting NG HUI WEN :

> Dear Mark and Justin,
>
>
>
> I have a potentially silly question here. I have been trying to work out
> the figures from the various options of g_energy. You mentioned before
> that the bonded terms are not decomposable/require some hacking with the
> .top file. I am a bit confused with that.
>
>
>
> As mentioned previously, I did
>
> 1)grompp -f new.mdp -n index.ndx -c old.tpr -o rerun1.tpr -p topol.top
>
> Where energy groups are added to the .mdp file
>
>
>
> 2)tpbconv -s rerun1.tpr -n index -o rerun2.tpr -nsteps 0
>
> To produce individual .tpr files for i) System  ii) Protein only  iii)
> Lipid only  iv) solv_ion only  v) protein_lipid  vi) protein_solv_ion
> vii) lipid_solv_ion
>
>
>
> 3)trjconv  -f old.trr  -n index.ndx  -s rerun2.tpr  -o rerun.trr
>
> To produce a corresponding .trr files for (i) to (vii) in step 2
>
>
>
> 4) mdrun -s rerun2.tpr  -rerun  rerun.trr
>
> To produce the .edr files for (i) to (vii)
>
>
>
> With g_energy I derived these different components for (i) to (vii):
>
> a-PE
>
> b-Angle (lipid)/G96 angle (protein)
>
> c-Proper dihedral
>
> d-Improper dihedral
>
> e-Ryckaert Belleman (lipid)
>
> f-LJ 1-4
>
> g-Coul 1-4
>
> h-L J SR
>
> i-Disp. Corr
>
> j-Coul SR
>
> k-Coul. Recip
>
>
>
> After doing some maths, I got the below:
>
> 1)  the PEs for (i) to (vii) are the sum of their corresponding b-k
> values
>
> e.g. the PE for the system =  Angle (lipid) + G96 angle (protein) +
> Prop. Dihedral + imp dihedral + Ryckaert Belleman (lipid) + LJ14 + Coul
> 1-4 + LJ SR + Disp Corr + Coul SR + Coul recip.
>
> 2)  For bonded terms such as proper dihedral, I found that the
> proper dihedral of the system (i) = (ii) + (iii) i.e sum of proper
> dihedral values from protein and lipid. The same goes for the improper
> dihedral term. This is where I am confused. Doesn't this show that the
> bonded terms can be decomposed?
>
>
>
> I realize there has been a rather long pause between this email and the
> last, sorry about that, it's because I have been trying to work out
> myself why you say the bonded terms cannot be decomposed easily.
>
>

The bonded terms can be decomposed by the procedure you've gone through.  I (and
others) always caution against thinking that the simple use of energygrps will
do the trick.  An iterative approach is indeed required.

>
> Perhaps as Justin pointed out, it is probably not worth the effort to
> derive individual energies of the various components that make up my
> system, but I would really appreciate a reply on this before I put the
> matter to rest. Thanks!
>

I still do not see the value of trying to claim "the energy of the protein is
(some number)" by decomposing various potential energy terms.  The PME term
cannot be decomposed, for one.  Even though you've gotten a value of Coul-recip
for your various calculations, I don't know how valid the results are.

-Justin

>
>
> HW
>
>
>
>
>
> From: gmx-users-boun...@gromacs.org
> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham
> Sent: Friday, November 12, 2010 12:32 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] mdrun -rerun: bonded interactions of protein
>
>
>
> On 11/11/2010 7:46 PM, NG HUI WEN wrote:
>
> Thanks a lot Justin and Mark for your useful input.
>
>
>
> Indeed Justin was right, the quest to dissect the total energy of the
> system to get that contributed by the protein alone was not trivial at
> all!
>
>
> Indeed. If I'd observed you were doing PME, I'd have made the same
> point.
>
>
>
>
> I missed out this thread yesterday
> http://www.mail-archive.com/gmx-users@gromacs.org/msg34610.html as well
> as Mark's trick to decompose bonded terms by hacking the .top file.
> (However, I read from
> http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy that the
> Coul-recip term is not decomposable regardless of the tricks used...)
>
>
>
> Mark, following your advice, I added -nsteps 0 (-1 didn't work) to
> tpbconv. I managed to get the interactive prompt succesfully this time.
>
>
> Yes, nsteps=-1 is a GROMACS 4.5-ism, sorry.
>
>
>
>
> Reading toplogy and shit from rerun1.tpr
> Reading file rerun1.tpr, VERSION 4.0.7 (single precision)
> Setting nsteps to 0
> Group 0 (  System) has 100581 elements
> Group 1 ( Protein) has  4002 elements
> Group 2 (   Protein-H) has  3145 elements
> Group 3 ( C-alpha) has   412 elements
> Group 4 (Backbone) has  1236 elements
> Group 5 (   MainChain) has  1649 elements
> Group 6 (MainChain+Cb) has  2027 elements
> Group 7 ( MainChain+H) has  2039 elements
> Group 8 (   SideChain) has  1963 elements
> Group 9 ( SideChain-H) has  1496 elements
> Group10 ( Prot-Masses) has  4002 elements
> Group11 ( Non-Protein) has 96579 elements
> Group12 (POPE) has 13052 elements
> Group13 ( SOL) has 83523 elements
> Group14 ( CL-) has 4 elements
> Group15 (   Other) has 96579 elements
> Group

[gmx-users] two problems with gromacs 4.5.3

[Sanku M]

Hi,

When using gromacs 4.5.3, I experienced two problems ( neither of which exist 
in 
gromacs 4.0.7 or older version like 3.3.3)
  1. when issuing grompp command to start one of my  simulations, gromacs 4.5.3 
gives me fatal error:
  'can not find atom type SNa .'
  However, with gromacs 4.0.7 and gromacs 3.3.3, for the  same simulation , 
grompp runs smoothly ( as atom type SNa indeed exist in my directory).
I am not sure what is wrong with grompp in gromacs 4.5.3

2. when using g_density command , after processing data , gromacs 4.5.3 gives 
an 
error :
*** glibc detected *** double free or corruption (out): 0x006d8ce0 ***
Aborted

But, the same g_density with gromacs 4.0.7 and gromacs 3.3.3 works smoothly.

Any idea  will be appreciated .
Sanku


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Re: [gmx-users] two problems with gromacs 4.5.3

[Roland Schulz]

On Mon, Nov 22, 2010 at 2:55 PM, Sanku M  wrote:

> Hi,
>
> When using gromacs 4.5.3, I experienced two problems ( neither of which
> exist in gromacs 4.0.7 or older version like 3.3.3)
>   1. when issuing grompp command to start one of my  simulations, gromacs
> 4.5.3 gives me fatal error:
>   'can not find atom type SNa .'
>   However, with gromacs 4.0.7 and gromacs 3.3.3, for the  same simulation ,
> grompp runs smoothly ( as atom type SNa indeed exist in my directory).
> I am not sure what is wrong with grompp in gromacs 4.5.3
>

The folder layout for the input files has changed. Make sure you have the
files in the correct location for 4.5.3.

>
> 2. when using g_density command , after processing data , gromacs 4.5.3
> gives an error :
> *** glibc detected *** double free or corruption (out): 0x006d8ce0
> ***
> Aborted
>
> But, the same g_density with gromacs 4.0.7 and gromacs 3.3.3 works
> smoothly.
>

That seems to be a problem in g_density. Please open a bug on
bugzilla.gromacs.org with enough detail to reproduce the error.

Roland


>
> Any idea  will be appreciated .
> Sanku
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>



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865-241-1537, ORNL PO BOX 2008 MS6309
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Re: [gmx-users] protein folding

[Lutz Maibaum]

On Nov 22, 2010, at 3:09 AM, mohsen ramezanpour wrote:
> I am searching for a tutorial for  learning how to do protein folding with 
> Gromacs.
> Do any one know such tutorials?

Not exactly a tutorial, but you can find Gromacs input files, as well as 
several hundreds of microseconds worth of MD trajectories of a fast-folding 
protein, on this website:

http://simtk.org/home/foldvillin

Together with the publication that goes with it, this might be a good start to 
read about protein folding simulations. It's not something you can easily 
reproduce on your desktop, though.

Hope this helps,

  Lutz

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RE: [gmx-users] mdrun -rerun: bonded interactions of protein

[NG HUI WEN]

Thanks a lot for that Justin - I fully appreciate your point, thanks
again!

-Original Message-
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Tuesday, November 23, 2010 3:29 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] mdrun -rerun: bonded interactions of protein

Quoting NG HUI WEN :

> Dear Mark and Justin,
>
>
>
> I have a potentially silly question here. I have been trying to work
out
> the figures from the various options of g_energy. You mentioned before
> that the bonded terms are not decomposable/require some hacking with
the
> .top file. I am a bit confused with that.
>
>
>
> As mentioned previously, I did
>
> 1)grompp -f new.mdp -n index.ndx -c old.tpr -o rerun1.tpr -p topol.top
>
> Where energy groups are added to the .mdp file
>
>
>
> 2)tpbconv -s rerun1.tpr -n index -o rerun2.tpr -nsteps 0
>
> To produce individual .tpr files for i) System  ii) Protein only  iii)
> Lipid only  iv) solv_ion only  v) protein_lipid  vi) protein_solv_ion
> vii) lipid_solv_ion
>
>
>
> 3)trjconv  -f old.trr  -n index.ndx  -s rerun2.tpr  -o rerun.trr
>
> To produce a corresponding .trr files for (i) to (vii) in step 2
>
>
>
> 4) mdrun -s rerun2.tpr  -rerun  rerun.trr
>
> To produce the .edr files for (i) to (vii)
>
>
>
> With g_energy I derived these different components for (i) to (vii):
>
> a-PE
>
> b-Angle (lipid)/G96 angle (protein)
>
> c-Proper dihedral
>
> d-Improper dihedral
>
> e-Ryckaert Belleman (lipid)
>
> f-LJ 1-4
>
> g-Coul 1-4
>
> h-L J SR
>
> i-Disp. Corr
>
> j-Coul SR
>
> k-Coul. Recip
>
>
>
> After doing some maths, I got the below:
>
> 1)  the PEs for (i) to (vii) are the sum of their corresponding
b-k
> values
>
> e.g. the PE for the system =  Angle (lipid) + G96 angle (protein) +
> Prop. Dihedral + imp dihedral + Ryckaert Belleman (lipid) + LJ14 +
Coul
> 1-4 + LJ SR + Disp Corr + Coul SR + Coul recip.
>
> 2)  For bonded terms such as proper dihedral, I found that the
> proper dihedral of the system (i) = (ii) + (iii) i.e sum of proper
> dihedral values from protein and lipid. The same goes for the improper
> dihedral term. This is where I am confused. Doesn't this show that the
> bonded terms can be decomposed?
>
>
>
> I realize there has been a rather long pause between this email and
the
> last, sorry about that, it's because I have been trying to work out
> myself why you say the bonded terms cannot be decomposed easily.
>
>

The bonded terms can be decomposed by the procedure you've gone through.
I (and
others) always caution against thinking that the simple use of
energygrps will
do the trick.  An iterative approach is indeed required.

>
> Perhaps as Justin pointed out, it is probably not worth the effort to
> derive individual energies of the various components that make up my
> system, but I would really appreciate a reply on this before I put the
> matter to rest. Thanks!
>

I still do not see the value of trying to claim "the energy of the
protein is
(some number)" by decomposing various potential energy terms.  The PME
term
cannot be decomposed, for one.  Even though you've gotten a value of
Coul-recip
for your various calculations, I don't know how valid the results are.

-Justin

>
>
> HW
>
>
>
>
>
> From: gmx-users-boun...@gromacs.org
> [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Mark Abraham
> Sent: Friday, November 12, 2010 12:32 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] mdrun -rerun: bonded interactions of protein
>
>
>
> On 11/11/2010 7:46 PM, NG HUI WEN wrote:
>
> Thanks a lot Justin and Mark for your useful input.
>
>
>
> Indeed Justin was right, the quest to dissect the total energy of the
> system to get that contributed by the protein alone was not trivial at
> all!
>
>
> Indeed. If I'd observed you were doing PME, I'd have made the same
> point.
>
>
>
>
> I missed out this thread yesterday
> http://www.mail-archive.com/gmx-users@gromacs.org/msg34610.html as
well
> as Mark's trick to decompose bonded terms by hacking the .top file.
> (However, I read from
> http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy that
the
> Coul-recip term is not decomposable regardless of the tricks used...)
>
>
>
> Mark, following your advice, I added -nsteps 0 (-1 didn't work) to
> tpbconv. I managed to get the interactive prompt succesfully this
time.
>
>
> Yes, nsteps=-1 is a GROMACS 4.5-ism, sorry.
>
>
>
>
> Reading toplogy and shit from rerun1.tpr
> Reading file rerun1.tpr, VERSION 4.0.7 (single precision)
> Setting nsteps to 0
> Group 0 (  System) has 100581 elements
> Group 1 ( Protein) has  4002 elements
> Group 2 (   Protein-H) has  3145 elements
> Group 3 ( C-alpha) has   412 elements
> Group 4 (Backbone) has  1236 elements
> Group 5 (   MainChain) has  1649 elements
> Group 6 (MainChain+Cb) has  2027 elements
> Group 7 ( MainChain+H) has  2039 elements
> Group 8 (   SideChain) has  196

[gmx-users] Implementation of Andersen Thermostat

[sapna sarupria]

Dear All,

I was just wondering if Andersen thermostat is implemented or going to be
implemented in the recent/forthcoming versions of Gromacs.

Is there anyone who has done it otherwise and would be willing to share an
outline of the subroutines that they modified?

Thanks in advance for your help,

Regards
Sapna
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RE: [gmx-users] find the relevant structure out

[#ZHAO LINA#]

I really do not know how to get those beta-sheet structures out,
or maybe by which ways?

Any clues are warmly welcomed and appreciated.

lina

From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Mark Abraham [mark.abra...@anu.edu.au]
Sent: Sunday, November 21, 2010 11:58 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] find the relevant structure out

On 21/11/2010 11:43 PM, #ZHAO LINA# wrote:
Hi,

I had done 10ns simulation,

by dssp, can see the beta-sheet appeared very apparently, before it's 
alpha-helix.

there were 5000 frames, I based on the time of the picture got from dssp, I can 
guess around which frames is supposed to have those beta sheets.

After I took few frames which I thought might be representive, but under pymol, 
show cartoon, there is none beta sheet at all. There were 5000 frames, I really 
do not know which one is most representive.

Or maybe some parts I understand wrong.

Thanks for any advice and if I am wrong please let me know,

We've really no idea of the detail of what you've done, so can't guess. Just 
about anything could be the problem - all the way from "you are looking at the 
wrong files", to "pymol's definition of a beta sheet doesn't agree with dssp".

If you can't report the command lines you used easily, then your method was not 
reproducible enough, or not recorded well enough :-)

Mark
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Re: [gmx-users] grompp error version 4.5.2

[Adva Suez]

my command was:

/share/apps/gromacs-4.5.2/bin/grompp_mpi -f md.mdp -c
../../membed_17_npt.gro.884814.gro -t ../../membed_17_npt.trr.884814.trr -e
../../membed_17_npt.edr.884814.edr -p topol_protein_dppc_sol3_22.top -n
index.ndx -o md_0_1_22.tpr

the name of the edr file (and other NPT outputs) is because i'm running it
in qsub and therefore it contains the job id... that's all.

Do you have any solution?

Thanks,
Adva

On Mon, Nov 22, 2010 at 2:10 PM, Mark Abraham wrote:

>  On 22/11/2010 11:03 PM, Adva Suez wrote:
>
> Hello,
> I'm using your KALP in DPPC tutorial to figure out how to simulate a
> molecule in a membrane in GROMACS. I'm using version 4.5.2 and from some
> reason I got an error in grompp whe trying generate md_0_1.tpr.
> the error is:
>
> Program grompp_mpi, VERSION 4.5.2
> Source code file: enxio.c, line: 1097
>
> Fatal error:
> Could not find frame with time 1000.61 in
> '../../membed_17_npt.edr.884814.edr'
>
>
> That's a seriously weird .edr file name. What was your command line?
>
> Mark
>
>
> This is weird because I only have 1000 frames in the NPT run...
> Can you please help me?
>
> Thanks,
> Adva.
>
>
> --
> Adva Yeheskel
> Bioinformatics Unit
> Rm 001, Sherman bldg.,
>  G.S.W. Faculty of Life Sciences
>  Tel-Aviv University, ISRAEL 69978
>
>  Tel: 972-3-6406840; Fax: 972-3-6405098
>  E-mail: sueza...@tauex.tau.ac.il
>  Web-site:
> http://www.tau.ac.il/lifesci/bioinformatics.html
>
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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-- 
Adva Yeheskel
Bioinformatics Unit
Rm 001, Sherman bldg.,
 G.S.W. Faculty of Life Sciences
 Tel-Aviv University, ISRAEL 69978

 Tel: 972-3-6406840; Fax: 972-3-6405098
 E-mail: sueza...@tauex.tau.ac.il
 Web-site:
http://www.tau.ac.il/lifesci/bioinformatics.html
-- 
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