Re: [gmx-users] P4_error for extending coarse grained MD simulations

[张春雷]

The last .gro file only provides coordinates of the system. No velocity is
recorded. Actually, what I attempt to achieve is a binary identical
trajectory. So I think the velocity from the last step is critical.

I have tried another approach in which the checkpoint file is neglected.

$mdrun_mpi_d -s md_720ns.tpr  -e md_720ns.edr -o md_720ns.trr -g
md_720ns.log

It works. So the checkpoint file appears to contain some error. But it is
generated by a normally finished production simulation.
Have  you encountered similar things?

Thank you for your suggestions!



在 2010年6月25日 上午9:16，weixin 写道：

>
> How about using the last .gro file to continue your simulation?
>
>
>
> 2010/6/24 张春雷 
>
>> Dear GMX-users,
>>
>> This is Justin.
>> I am performing coarse-grained simulation on a protein-lipid bilayer
>> system. This is a MARTINI CG model.
>> I have successfully completed a 360ns simulation, during which the time
>> step is 30 fs.
>>
>> I would like to extend the simulation to 1micro-second. The commands I
>> used are:
>>
>> $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr
>>
>> $mdrun_mpi_d -s md_720ns.tpr  -append -e md_360ns.edr -o md_360ns.trr -g
>> md_360ns.log -cpi state.cpt
>>
>> However, I received the following message:
>>
>> Checkpoint file is from part 1, new output files will be suffixed
>> part0002.
>> Getting Loaded...
>> Reading file md_720ns.tpr, VERSION 4.0.3 (double precision)
>>
>> Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010
>>
>> Loaded with Money
>>
>> starting mdrun 'Protein in POPE bilayer'
>> 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps).
>> step 1200, remaining runtime: 0 s
>> p0_6991:  p4_error: interrupt SIGSEGV: 11
>>
>> I have searched the mail-list, but found no similar report. I also search
>> through google, but no answer seems satisfactory.
>>
>> I once performed extending simulation for all atom simulation, and the
>> method mentioned above worked.
>>
>> Is anyone familiar with MARTINI CG simulation?
>> Could you give me some suggestions?
>>
>> Many thanks!
>>
>> Justin
>>
>> --
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>
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[gmx-users] .RTP files

[P.R.Anand Narayanan]

Dear gromacs users,
I have been trying to use a polymer in the system and for its topology 
generation I have created its .rtp file. I am having trouble using the .rtp 
file in pdb2gmx command as it shows "file input/output error". Can anyone 
please help me as to how i should use the .rtp file in the pdb2gmx command to 
retrieve the topology files? 

Thanking you,
Regards,
Anand


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[gmx-users] Re: vdwtype=shift

[you zou]

Thank you for your help friends, But I have no any idea about amount of 
rvdw-switch. I would like to use vdwtype=shift(shift LJ to 0), but I don't know 
which number for rvdw-switch and rvdw should be choice? In manual I saw 
rvdw-switch=0 and rvdw=1.0, but it had this error. section 7.3.11 of gromacs 
manual (v4.0)/

-Gaurav

On Thu, Jun 24, 2010 at 4:40 AM, Erik Marklund  wrote:
> you zou skrev:
>>
>> Dear users,
>>
>> I have a question about vdwtype. My question is if I use vdwtype=shift in
>> nvt.mdp file:
>>
>> ; Neighborsearching
>> ns_type = grid ; search neighboring grid cels
>> nstlist = 5 ; 10 fs
>> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
>> rcoulomb = 1.0   ; short-range electrostatic cutoff (in nm)
>> ; Method for doing Van der Waals
>> vdwtype = shift
>> ; cut-off lengths   rvdw-switch  = 0
>> rvdw = 0.9,
>>
>> I have this error:
>> Fatal error:
>> With dispersion correction rvdw-switch can not be zero for vdw-type =
>> Shift
>>
>> That I don't know how can I solve this problem.
>>
>> Thank you
>> 
>> Hotmail: Powerful Free email with security by Microsoft. Get it now.
>> 
>
> Errr... Setting rvdw-switch to a non-zero value might be worth trying.
>
> --

  
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Re: [gmx-users] P4_error for extending coarse grained MD simulations

[weixin]

How about using the last .gro file to continue your simulation?



2010/6/24 张春雷 

> Dear GMX-users,
>
> This is Justin.
> I am performing coarse-grained simulation on a protein-lipid bilayer
> system. This is a MARTINI CG model.
> I have successfully completed a 360ns simulation, during which the time
> step is 30 fs.
>
> I would like to extend the simulation to 1micro-second. The commands I used
> are:
>
> $tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr
>
> $mdrun_mpi_d -s md_720ns.tpr  -append -e md_360ns.edr -o md_360ns.trr -g
> md_360ns.log -cpi state.cpt
>
> However, I received the following message:
>
> Checkpoint file is from part 1, new output files will be suffixed part0002.
> Getting Loaded...
> Reading file md_720ns.tpr, VERSION 4.0.3 (double precision)
>
> Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010
>
> Loaded with Money
>
> starting mdrun 'Protein in POPE bilayer'
> 2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps).
> step 1200, remaining runtime: 0 s
> p0_6991:  p4_error: interrupt SIGSEGV: 11
>
> I have searched the mail-list, but found no similar report. I also search
> through google, but no answer seems satisfactory.
>
> I once performed extending simulation for all atom simulation, and the
> method mentioned above worked.
>
> Is anyone familiar with MARTINI CG simulation?
> Could you give me some suggestions?
>
> Many thanks!
>
> Justin
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] standard state correction of delta G from a PMF

[chris . neale]

Dear Elio:

I think I was pretty clear in my last email:

If you still have trouble, then your next post should include things
like "I tried this... but I didn't understand this specific part"
to make it clear that you have put in the effort here.

Otherwise, hopefully somebody else has the time to help you.

Chris.

-- original message --

Hi Chris. Thanks for getting back to me. My problem is with the  
conversion to standard state concentration (1M) from umbrella sampling  
simulations. I can't understand how to do this from my umbrella  
sampling simulations. Even after reading several papers that perform  
the correction unclear on what is going on.


Elio Cino

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Re: [gmx-users] Problems with installing mpi-version of Gromacs on Cluster with Debian-Lenny

[Mark Abraham]

- Original Message -
From: Christian Mücksch 
Date: Friday, June 25, 2010 0:21
Subject: [gmx-users] Problems with installing mpi-version of Gromacs on Cluster 
with Debian-Lenny
To: MAILINGLIST GROMACS 

> Dear All,
> 
> I've been trying to compile and get Gromacs (version 4.0.7) 
> working on a cluster that runs with Debian Lenny.
> 
> I set the following variables:
> export SOFT=$HOME/GROMACS
> export PATH="$PATH":$SOFT/bin
> export LDFLAGS="-L$SOFT/lib"
> export CPPFLAGS="-I$SOFT/include"
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$SOFT/lib
> export MPICC=$SOFT/bin/mpicc
> 
> and then did
> 
> ./configure --prefix=$SOFT --disable-float --program-
> suffix=_mpi_d --enable-mpi
> 
> after I installed the Gromacs-version without mpi. Before 
> configuring Gromacs I compiled the latest version of OPEN-MPI 
> with gcc-4.3.
> I did exactly the same on another cluster that runs with Debian 
> Etch and everything worked fine and was pretty straightforward.
> 
> Here I get the following error during configuring:
> 
> checking whether your compiler can handle assembly files 
> (*.s)... no
> configure: error: Upgrade your compiler (or disable assembly loops)
> 
> The exact error from the config.log looks like this:
> 
> configure:32822: checking whether your compiler can handle 
> assembly files (*.s)
> configure:32841: /usr/bin/mpicc  -O3 -fomit-frame-pointer -
> finline-functions -Wall -Wno-unused -funroll-all-loops -c 
> conftestasm.sconftestasm.s: Assembler messages:
> conftestasm.s:2: Error: bad register name `%rsp'
> configure:32844: $? = 1
> configure:32857: result: no
> configure:32859: error: Upgrade your compiler (or disable 
> assembly loops).
> 
> When I compiled Gromacs with the --disable-x86-64-sse option, 
> then my submitted jobs run extremely slow compared to the other 
> cluster.Although MPI is running and the CPU-loads are all 100% 
> the speed is nearly as slow as running on a single CPU.
> I also tried compiling with MVAPICH with is already installed on 
> the cluster but I get the same error.
> 
> Unfortunately I could not compile OPEN-MPI with the follwing flags:
> export CC="gcc-4.3 -m64"
> export CXX="g++-4.3 -m64"
> export F77="gfortran-4.3 -m64"
> 
> Do you have any idea what could be the cause of the problem so 
> that I can tell the Cluster-Admin what specific package to install?
> Any help would be deeply appreciated since I'm new to this whole 
> MPI topic and I could not find a way around this problem.

Your version of gcc isn't able to deal with the assembly code used by GROMACS 
to get its speed. Three solutions come to mind:
1) Upgrade gcc - it is a compiler collection, and the gcc module on Debian 
looks to me like it has only the C compiler in it. The GNU assembler is in the 
binutils package, so installing that looks like the first place to start/check.
2) Compile for this architecture on some machine that has a better set of tools 
for compiling for scientific  applications.
3) Cross-compile for this architecture on some such machine.

Mark


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Re: [gmx-users] vdwtype=shift

[Gaurav Goel]

section 7.3.11 of gromacs manual (v4.0)/

-Gaurav

On Thu, Jun 24, 2010 at 4:40 AM, Erik Marklund  wrote:
> you zou skrev:
>>
>> Dear users,
>>
>> I have a question about vdwtype. My question is if I use vdwtype=shift in
>> nvt.mdp file:
>>
>> ; Neighborsearching
>> ns_type = grid ; search neighboring grid cels
>> nstlist = 5 ; 10 fs
>> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
>> rcoulomb = 1.0   ; short-range electrostatic cutoff (in nm)
>> ; Method for doing Van der Waals
>> vdwtype         = shift
>> ; cut-off lengths       rvdw-switch              = 0
>> rvdw                     = 0.9,
>>
>> I have this error:
>> Fatal error:
>> With dispersion correction rvdw-switch can not be zero for vdw-type =
>> Shift
>>
>> That I don't know how can I solve this problem.
>>
>> Thank you
>> 
>> Hotmail: Powerful Free email with security by Microsoft. Get it now.
>> 
>
> Errr... Setting rvdw-switch to a non-zero value might be worth trying.
>
> --
> ---
> Erik Marklund, PhD student
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,    75124 Uppsala, Sweden
> phone:    +46 18 471 4537        fax: +46 18 511 755
> er...@xray.bmc.uu.se    http://folding.bmc.uu.se/
>
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[gmx-users] standard state correction of delta G from a PMF

[Elio Cino]

Hi Chris. Thanks for getting back to me. My problem is with the conversion to 
standard state concentration (1M) from umbrella sampling simulations. I can't 
understand how to do this from my umbrella sampling simulations. Even after 
reading several papers that perform the correction unclear on what is going on. 

Elio Cino


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[gmx-users] Help with g_vanhove

[Juan M Vanegas]

Dear gmx users,

I am trying to calculate the Van Hove correlation function (G(r,t)) 
using the utility g_vanhove. However, I don't seem to be able to make it 
work. The program outputs files, but the points are all 0 except at r=0. 
My simulation is a hydrated lipid bilayer with 128 molecules. I have 
tried selecting whole molecules, single atoms, pairs of atoms but they 
show no difference. I tried looking at the source code to see if 
anything obvious would pop up, but there are no comments on any of the 
functions so it's pretty difficult figuring out what it does. I'm using 
gromacs 4.0.7. Any help would be appreciated.


Juan M. Vanegas
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[gmx-users] Weird error with g_sorient

[Justin A. Lemkul]

Hi All,

I'm trying to use g_sorient to calculate some solvent properties in a few 
systems I'm simulating.  It's the first time I've used the tool, so if I've 
missed something obvious, please let me know.  I'm getting a very weird error 
when I execute the command:


echo 1 13 | g_sorient_4.0.7_s -s md_0_20.tpr -f md_0_20.xtc -rmin 0 -rmax 1 -com

Groups 1 and 13 represent Protein (which is a single amino acid, dipeptide form) 
and SOL, respectively.  The error is:


---
Program g_sorient_4.0.7_s, VERSION 4.0.7
Source code file: mshift.c, line: 635

Fatal error:
No GREY nodes found while nG=1

---

I think I have tracked the problem down to time 958 ps.  If I supply -e 956 to 
the above command, the program finishes.  If I use -e 958, it crashes with the 
error.  However, if I run:


echo 1 13 | g_sorient_4.0.7_s -s md_0_20.tpr -f md_0_20.xtc -rmin 0 -rmax 1 -com 
-b 950 -e 1000


The program completes.  Very weird.  Using gmxcheck indicates no abnormality in 
the trajectory, and other analysis tools work just find (g_hbond, g_traj, g_rdf, 
etc).  Processing the frame at 958 ps (as a .gro file) also works fine, i.e.:


echo 1 13 | g_sorient_4.0.7_s -s md_0_20.tpr -f 958.gro -rmin 0 -rmax 1 -com

Works without a problem.

Does anyone know what's going on?  I found nothing about this in the archive. 
It seems that the failing function has something to do with correcting 
periodicity (?), but even if I use a trajectory that has been processed with 
trjconv -pbc mol I get the same failure.


-Justin

--


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] Making a .rtp file

[Justin A. Lemkul]

Amanda Watkins wrote:
I am trying to create a .gro file of a single detergent which I am going 
to then multiply and put it in water and have it form micelles. In order 
to create a .gro file, I know I need to create a .rtp file of my residue 


You do not *need* a .gro file, nor do you necessarily have to produce it using 
pdb2gmx.


http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#On_the_need_for_a_.gro_file

You do, however, need a topology, so pdb2gmx is one approach, yes.

or add it to the desired force field .rtp file I want to run my 
detergent in. Is there any way to custom make one (or add it to an 
existing .rtp) using data that I took from another program that I used 
to analyze and minimize my detergent? I am currently trying to create a 


Certainly.  See the manual for the .rtp file format specifications, or write the 
topology by hand.  Chapter 5 of the manual is a must-read.


.rtp and a .top file using x2top, but that still might not enable me to 
generate a .gro file. Thank you for taking the time to read my email and 
help me answer my question.




Does x2top give you a topology, though?  That's the hard part.  See the above 
link regarding .gro files.


-Justin

--


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] g_anaeig -proj

[Carla Jamous]

Hi everyone,

please I'm doing for the first time a covariance analysis.
I followed this tutorial:
http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html

But I don't understand. -proj gives the projection of the trajectory on the
first eigenvector, so I was expecting to have new coordinates for each atom
or each residue. Instead, I get a .xvg file saying:
""projection on eigenvectors (nm)"
@ xaxis  label "Time (ps)"
yaxis  label "vec 1"

Please can anyone tell me what this actually means? What data is in
nanometers? What does gromacs project?

Sorry if my question is stupid, but I can't find the answer.

Thank you.

Carla
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[gmx-users] Making a .rtp file

[Amanda Watkins]

I am trying to create a .gro file of a single detergent which I am going to 
then multiply and put it in water and have it form micelles. In order to create 
a .gro file, I know I need to create a .rtp file of my residue or add it to the 
desired force field .rtp file I want to run my detergent in. Is there any way 
to custom make one (or add it to an existing .rtp) using data that I took from 
another program that I used to analyze and minimize my detergent? I am 
currently trying to create a .rtp and a .top file using x2top, but that still 
might not enable me to generate a .gro file. Thank you for taking the time to 
read my email and help me answer my question.



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[gmx-users] Problems with installing mpi-version of Gromacs on Cluster with Debian-Lenny

[Christian Mücksch]

Dear All,

I've been trying to compile and get Gromacs (version 4.0.7) working on a 
cluster that runs with Debian Lenny.


I set the following variables:
export SOFT=$HOME/GROMACS
export PATH="$PATH":$SOFT/bin
export LDFLAGS="-L$SOFT/lib"
export CPPFLAGS="-I$SOFT/include"
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$SOFT/lib
export MPICC=$SOFT/bin/mpicc

and then did

./configure --prefix=$SOFT --disable-float --program-suffix=_mpi_d 
--enable-mpi


after I installed the Gromacs-version without mpi. Before configuring 
Gromacs I compiled the latest version of OPEN-MPI with gcc-4.3.
I did exactly the same on another cluster that runs with Debian Etch and 
everything worked fine and was pretty straightforward.


Here I get the following error during configuring:

checking whether your compiler can handle assembly files (*.s)... no
configure: error: Upgrade your compiler (or disable assembly loops)

The exact error from the config.log looks like this:

configure:32822: checking whether your compiler can handle assembly 
files (*.s)
configure:32841: /usr/bin/mpicc  -O3 -fomit-frame-pointer 
-finline-functions -Wall -Wno-unused -funroll-all-loops -c conftestasm.s

conftestasm.s: Assembler messages:
conftestasm.s:2: Error: bad register name `%rsp'
configure:32844: $? = 1
configure:32857: result: no
configure:32859: error: Upgrade your compiler (or disable assembly loops).

When I compiled Gromacs with the --disable-x86-64-sse option, then my 
submitted jobs run extremely slow compared to the other cluster.
Although MPI is running and the CPU-loads are all 100% the speed is 
nearly as slow as running on a single CPU.
I also tried compiling with MVAPICH with is already installed on the 
cluster but I get the same error.


Unfortunately I could not compile OPEN-MPI with the follwing flags:
export CC="gcc-4.3 -m64"
export CXX="g++-4.3 -m64"
export F77="gfortran-4.3 -m64"

Do you have any idea what could be the cause of the problem so that I 
can tell the Cluster-Admin what specific package to install?
Any help would be deeply appreciated since I'm new to this whole MPI 
topic and I could not find a way around this problem.


Thanks a lot,
Christian

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[gmx-users] P4_error for extending coarse grained MD simulations

[张春雷]

Dear GMX-users,

This is Justin.
I am performing coarse-grained simulation on a protein-lipid bilayer system.
This is a MARTINI CG model.
I have successfully completed a 360ns simulation, during which the time step
is 30 fs.

I would like to extend the simulation to 1micro-second. The commands I used
are:

$tpbconv_mpi_d -s md_360ns.tpr -extend 36 -o md_720ns.tpr

$mdrun_mpi_d -s md_720ns.tpr  -append -e md_360ns.edr -o md_360ns.trr -g
md_360ns.log -cpi state.cpt

However, I received the following message:

Checkpoint file is from part 1, new output files will be suffixed part0002.
Getting Loaded...
Reading file md_720ns.tpr, VERSION 4.0.3 (double precision)

Reading checkpoint file state.cpt generated: Mon Jun 14 09:48:10 2010

Loaded with Money

starting mdrun 'Protein in POPE bilayer'
2400 steps, 72.0 ps (continuing from step 1200, 36.0 ps).
step 1200, remaining runtime: 0 s
p0_6991:  p4_error: interrupt SIGSEGV: 11

I have searched the mail-list, but found no similar report. I also search
through google, but no answer seems satisfactory.

I once performed extending simulation for all atom simulation, and the
method mentioned above worked.

Is anyone familiar with MARTINI CG simulation?
Could you give me some suggestions?

Many thanks!

Justin
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Re: [gmx-users] General Question

[Justin A. Lemkul]

pawan raghav wrote:

Dear GROMACS team members,

I have a general question about the GROMACS, actually I have used 
GROMACS for the simulation of 59 amino acids domain part of the protein 
containing within it. This domain lies in the position from 34-92 out of 
239 residues, this loop having only 12 residues similarity whose does 
not found any similarity in this region. I have an objective to predict 
the behaviour of such a large loop flexibility. So my question is that 
at what level of accuracy, the loop optimization and prediction would be 
correct. Is it possible to predict the loop structure on the basis of 
simulation or can predict the structure of unstructure loop of a 
protein? Please comment on this because some people criticising MD 


The ability to predict loop conformations (and protein conformations in general) 
is a function of both the force field and the conditions applied.  Different 
force fields (unfortunately) have different "preferences" for certain 
configurations.  Such is the limitation of what we do.  You may have to either 
conduct your simulations with different force fields to eliminate such a bias. 
At the very least, you need well-converged data.  That means either numerous 
simulations of sufficiently long trajectories, or apply techniques like REMD.


simulations prediction. Can we predict the folded loop of a protein by 
using simulation? if yes then tell me about the analysis methods in 
gromacs for loop particularly. One more question is about the "dt" that 


The type of analysis depends on what you know about your system.  Different 
structural analyses are certainly possible, but what might be more significant 
is the identification of known interactions within your structure (amino acid 
contacts, etc).


it can be possible to change the value of dt in .mdp file instead of 
0.002 ps to 0.003 if yes then what is the significance of this and what 
is the efeect of this on simulation?


Anything is possible.  You still have to demonstrate that your simulation is 
stable, energy is conserved, etc.  Pretty rare to see a 3 fs timestep.  If 
you're just trying to speed up your simulations, use virtual sites in 
conjunction with constraints and go straight for a 4-5 fs timestep.


-Justin


--
Pawan



--


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] Help in parametrisation

[Justin A. Lemkul]

onetwo wrote:

Thanks Justin for the help,

I have Manganese in my protein with other two ligands at the active site.
I am using GROMOS96 43a1 force field.

Mangnese may have topology similar to Magnesium 2+, What I found is that 


Assuming a transition metal "may" be similar to another species is probably a 
pretty poor assumption.  Prepare for lots of criticism if you proceed with that 
thought.


I need to do changes in ffG43a1.rtp and ffG43a1nb.itp. But how should I 
calculate the nonbond_params for ffG43a1nb.itp.




Refer to the other GROMOS papers for how they derive parameters for small 
molecules.  I've never seen a demonstration of transition metal parameterization 
under these force fields, though.  Perhaps you should be using an AMBER force 
field that contains Mn2+.  Any particular reason you think you need GROMOS?


For both the other two ligands which contains phosphate and enol groups, 
I was able to create topology using PRODRG server.


Please pay careful attention to the second paragraph here:

http://www.gromacs.org/index.php?title=Download_%26_Installation/Related_Software/PRODRG#Tips

-Justin



Regards

onetwo wrote:
 > Hello All,
 >
 > I am new in this field, and I want to do simulation study on one of 
the protein conatining a metal ion and study its ability to form 
co-oridnation bond with other ligand, which is not defined in GROMOS 
force field which I have tried. If this choice of force field is correct 
for such type of study ?

 >
 > I have read Gromacs Manual Chapter 5, also I am following this 
gromacs mailing list for quite some time to get a help on how to include 
a new metal ion or a new ligand in their simulation and they have been 
refered to refer to the 
http://www.gromacs.org/Documentation/How-tos/Parameterization,

 >
 > but in this its not mentioned that how to actually do parameterization
 >
 > neither in manual it has been told on how to generate it ( due 
apologies,,I know, I may be wrong )

 >

The manual will not cover every possible topic. Parameterization is 
described in the primary literature for the force field you wish you 
use. "GROMOS" is not very specific - there are numerous parameter sets 
within this class of force field.


 > and it is more difficult for a person like me who doesnt have much 
knowledge in this field, so if someone can please help me guiding how to 
do parameterisation, I know this is not a trivial task, but still help 
in this regard may help many other fellow users besides me.


Aside from telling you to read all the literature you can, there's not 
much more help anyone can do to help you. You haven't described very 
well what your system is. What kind of functional groups are in your 
ligand? If the functional groups are shared with existing parameters, 
then you'll have a rather easy time constructing a topology. What type 
of metal ion is it? If you're dealing with a transition metal, using a 
standard MM force field may not work very well. Note the "Exotic 
Species" heading on the page you quoted above.


-Justin

 > Thanks in advance
 >
 >

-- 

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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--


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] General Question

[pawan raghav]

Dear GROMACS team members,

I have a general question about the GROMACS, actually I have used GROMACS
for the simulation of 59 amino acids domain part of the protein
containing within it. This domain lies in the position from 34-92 out of 239
residues, this loop having only 12 residues similarity whose does not found
any similarity in this region. I have an objective to predict the behaviour
of such a large loop flexibility. So my question is that at what level of
accuracy, the loop optimization and prediction would be correct. Is it
possible to predict the loop structure on the basis of simulation or can
predict the structure of unstructure loop of a protein? Please comment on
this because some people criticising MD simulations prediction. Can we
predict the folded loop of a protein by using simulation? if yes then tell
me about the analysis methods in gromacs for loop particularly. One more
question is about the "dt" that it can be possible to change the value of dt
in .mdp file instead of 0.002 ps to 0.003 if yes then what is the
significance of this and what is the efeect of this on simulation?
-- 
Pawan
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Re: [gmx-users] vdwtype=shift

[Erik Marklund]

you zou skrev:

Dear users,

I have a question about vdwtype. My question is if I use vdwtype=shift 
in nvt.mdp file:


; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0   ; short-range electrostatic cutoff (in nm)
; Method for doing Van der Waals
vdwtype = shift
; cut-off lengths   
rvdw-switch  = 0

rvdw = 0.9,

I have this error:
Fatal error:
With dispersion correction rvdw-switch can not be zero for vdw-type = 
Shift


That I don't know how can I solve this problem.

Thank you   



Hotmail: Powerful Free email with security by Microsoft. Get it now. 



Errr... Setting rvdw-switch to a non-zero value might be worth trying.

--
---
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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[gmx-users] vdwtype=shift

[you zou]

Dear users,
I have a question about vdwtype. My question is if I use vdwtype=shift in 
nvt.mdp file:
; Neighborsearchingns_type  = grid  ; search neighboring 
grid celsnstlist   = 5 ; 10 fsrlist= 1.0
   ; short-range neighborlist cutoff (in nm)rcoulomb   = 1.0   ; 
short-range electrostatic cutoff (in nm); Method for doing Van der Waalsvdwtype 
= shift; cut-off lengths   rvdw-switch  = 0rvdw 
= 0.9,
I have this error:Fatal error:With dispersion correction rvdw-switch can not be 
zero for vdw-type = Shift
That I don't know how can I solve this problem.
Thank you 
_
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Re: [gmx-users] Problem on forming bonds

[Tsjerk Wassenaar]

Ni hao Kwee Hong,

These special links should be defined in the file specbond.dat. That
file you can find in the gromacs topology data directory. Have a look
at the linkage of iron, e.g.. Also check the manual/wiki/mailinglist
on 'specbond.dat' for more information.

Hope it helps,

Tsjerk

On Thu, Jun 24, 2010 at 9:05 AM, Kwee Hong  wrote:
> Hi.
>
> I'm trying to subject a metalloprotein bound to cadmium to a molecular
> dynamics. I've defined the cadmium ion in the atom type parameter file
> (ffGa56a6.atp) and residue database (ffG53a6.rtp). And the bond length and
> bond angle between the cadmium and sulphur of the metalloprotein had been
> define in the force field file, too (ffG53a6abon.itp). As special bond is
> expected to be formed between the sulphur of cysteine and the cadmium ions,
> I've added the relevant information into specbond.dat.
>
> But when I run the pdb2gmx, there is no entries in the [ bonds ] and [
> angles ] for those bond length and bond angle. I've attached a sample of the
> topology generated by pdb2gmx in the attachment. Please kindly refer to it.
> And of course, as there is no entries in those parameter, there was no
> cadmium-thiolate bond observed when I visualised the structure using pymol.
> So, does that mean that I would need to add them on manually?
>
> To proceed with my simulation, I added the values in [ bonds ] and [ angles
> ] manually. And as I do not have the relevant dihedral angle value from the
> literature, I've deleted those entries in my topology file and continue to
> prepare and subject the protein to energy minimization. During EM, the
> potential energy of the system started to remain constant at step 124 and
> eventually steepest descents converged to machine precision in 128 steps
> with the maximum force is on atom 279 which would be one of the cadmium ions
> in the system. When I visualised the system, one water molecule was found to
> attached with atom 279, so I deleted that water molecule and subject the
> system to em again. Yet the same thing occur after running for 49 steps.
> What had gone wrong with my system? Is that cadmium molecule had been
> running too far until it has gone out of the protein as water molecule are
> not suppose to come into the protein.
>
> Any suggestion is welcomed.
>
> Thanks in advance.
>
> Regards,
> Joyce
>
>
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands
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Re: [gmx-users] Re: gmx-users Digest, Vol 74, Issue 134

[Carsten Kutzner]

Amin,

maybe your MPI-enabled executable is called mdrun_mpi. Check
the directory where mdrun is and make shure (with ldd for example)
the mdrun* you are using is linked to the MPI library you are using.

Carsten



On Jun 24, 2010, at 6:51 AM, Amin Arabbagheri wrote:

> Carsten,
> 
> Thanks for your help, I used something like "mpirun -np 3 mdrun -s topol.tpr",
> it works but its something like repeating a single job 3 times, 
> simultaneously.
> here is the output on the screen :
> {
>  Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.1#
> 
> Back Off! I just backed up ener.edr to ./#ener.edr.1#
> 
> Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.2#
> 
> Back Off! I just backed up ener.edr to ./#ener.edr.2#
> 
> Back Off! I just backed up md_traj_dam_2nd.trr to ./#md_traj_dam_2nd.trr.3#
> 
> Back Off! I just backed up ener.edr to ./#ener.edr.3#
> starting mdrun 'Protein in water'
> 100 steps,   1000.0 ps.
> starting mdrun 'Protein in water'
> 100 steps,   1000.0 ps.
> starting mdrun 'Protein in water'
> 100 steps,   1000.0 ps.
> step 736900, will finish Fri Jun 25 07:45:04 2010
> }
> the estimated time is as long as one single job!
> 
> --- On Mon, 21/6/10, gmx-users-requ...@gromacs.org 
>  wrote:
> 
> From: gmx-users-requ...@gromacs.org 
> Subject: gmx-users Digest, Vol 74, Issue 134
> To: gmx-users@gromacs.org
> Date: Monday, 21 June, 2010, 9:03
> 
> Send gmx-users mailing list submissions to
> gmx-users@gromacs.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-requ...@gromacs.org
> 
> You can reach the person managing the list at
> gmx-users-ow...@gromacs.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
> 
> 
> Today's Topics:
> 
>1. (no subject) (Amin Arabbagheri)
>2. Re: (no subject) (Justin A. Lemkul)
>3. Re: (no subject) (Linus ?stberg)
>4. Re: (no subject) (Carsten Kutzner)
>5. Help with defining new residue (OXY--HEME) (Omololu Akin-Ojo)
>6. Re: Help with defining new residue (OXY--HEME) (Justin A. Lemkul)
> 
> 
> --
> 
> Message: 1
> Date: Mon, 21 Jun 2010 05:00:04 -0700 (PDT)
> From: Amin Arabbagheri 
> Subject: [gmx-users] (no subject)
> To: gmx-users@gromacs.org
> Message-ID: <180446.74209...@web50607.mail.re2.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi all,
> 
> I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic package 
> manager.
> I want to run a simulation in parallel on a multi processor, single PC, but 
> to compile via grompp, it doesn't accept -np flag, and also , using -np in 
> mdrun, it still runs as a single job.
> Thanks a lot for any instruction.
> 
> Bests,
> Amin
> 
> 
> 
> 
>   
> -- next part --
> An HTML attachment was scrubbed...
> URL: 
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20100621/fd800779/attachment-0001.html
> 
> --
> 
> Message: 2
> Date: Mon, 21 Jun 2010 08:05:15 -0400
> From: "Justin A. Lemkul" 
> Subject: Re: [gmx-users] (no subject)
> To: Discussion list for GROMACS users 
> Message-ID: <4c1f557b.4090...@vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 
> 
> 
> Amin Arabbagheri wrote:
> > Hi all,
> > 
> > I've installed GROMACS 4.0.7 and MPI libraries using ubuntu synaptic 
> > package manager.
> > I want to run a simulation in parallel on a multi processor, single PC, 
> > but to compile via grompp, it doesn't accept -np flag, and also , using 
> > -np in mdrun, it still runs as a single job.
> > Thanks a lot for any instruction.
> > 
> 
> Regarding grompp:
> 
> http://www.gromacs.org/Documentation/FAQs
> 
> As for mdrun, please provide your actual command line.  The mdrun -np flag is 
> nonfunctional, instead the number of nodes are taken from, i.e. mpirun -np 
> from 
> which mdrun is launched.
> 
> -Justin
> 
> > Bests,
> > Amin
> > 
> > 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> 
> 
> --
> 
> Message: 3
> Date: Mon, 21 Jun 2010 14:07:54 +0200
> From: Linus ?stberg 
> Subject: Re: [gmx-users] (no subject)
> To: Discussion list for GROMACS users 
> Message-ID:
> 
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Use grompp normally, without the -np flag. Then run mdrun_mpi with your
> normal parameters as mpirun -np x mdrun_mpi -deffnm xx
> 
> On Mon, Jun 21, 2010 at 2:00 PM, Amin Arabbagheri wrote:
> 
> > Hi all,

[gmx-users] Problem on forming bonds

[Kwee Hong]

Hi.

I'm trying to subject a metalloprotein bound to cadmium to a molecular
dynamics. I've defined the cadmium ion in the atom type parameter file
(ffGa56a6.atp) and residue database (ffG53a6.rtp). And the bond length and
bond angle between the cadmium and sulphur of the metalloprotein had been
define in the force field file, too (ffG53a6abon.itp). As special bond is
expected to be formed between the sulphur of cysteine and the cadmium ions,
I've added the relevant information into specbond.dat.

But when I run the pdb2gmx, there is no entries in the [ bonds ] and [
angles ] for those bond length and bond angle. I've attached a sample of the
topology generated by pdb2gmx in the attachment. Please kindly refer to it.
And of course, as there is no entries in those parameter, there was no
cadmium-thiolate bond observed when I visualised the structure using pymol.
So, does that mean that I would need to add them on manually?

To proceed with my simulation, I added the values in [ bonds ] and [ angles
] manually. And as I do not have the relevant dihedral angle value from the
literature, I've deleted those entries in my topology file and continue to
prepare and subject the protein to energy minimization. During EM, the
potential energy of the system started to remain constant at step 124 and
eventually steepest descents converged to machine precision in 128 steps
with the maximum force is on atom 279 which would be one of the cadmium ions
in the system. When I visualised the system, one water molecule was found to
attached with atom 279, so I deleted that water molecule and subject the
system to em again. Yet the same thing occur after running for 49 steps.
What had gone wrong with my system? Is that cadmium molecule had been
running too far until it has gone out of the protein as water molecule are
not suppose to come into the protein.

Any suggestion is welcomed.

Thanks in advance.

Regards,
Joyce


topol_sample
Description: Binary data
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