Re: [gmx-users] installation problem

[Mark Abraham]

Rafael Real Guerra wrote:

Hi

Well, let’s start saying that I’m new at Linux and I’m trying to start 
on Gromacs as well.


I’ve been trying to install Gromacs 4.0 in my computer (laptop ACER 
Aspire 4530, AMD Athlon 64X2) running Mandriva 2009 and I just got stuck 
at the very beginning.


4.0 is several months out of date already. Try 4.0.3 :-)

As Justin said, your issue is that you need a C compiler, as described 
here http://www.gromacs.org/content/view/23/33/. For your platform, a 
Fortran compiler is a needless complication.


Mark
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Re: [gmx-users] pdb2gmx: Bond type, Angle type, Dihedral angle type missing in topology file.

[Mark Abraham]

anoop dimri wrote:






Hi all gromacs users.

I am using gromacs v 3.3.3 on 32 bit system with suse-linux. I am 
working with protein and using Gromos96 43a1 force-field. When i 
generate topology file through pdb2gmx, i found that some bond types, 
angle types and Dihedral angle types are missing. Some of these are 
related to S-S bridge and remaining are related to HEME's Fe 
(intra-residual and inter-residual). Should I fill this manually in top 
file ? If   anyone know why this thing is happening, so please give me  
suggestion.


See http://wiki.gromacs.org/index.php/specbond.dat

Mark
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Re: [gmx-users] about dumping the last frame

[nahren manuel]

Dear Awasthi,
go through GROMACS Introductory tutorial...

trjconv -f abc.pdb -s abc.tpr -o 3frame.pdb -dump 3

You can also open the pdb file in VMD and save only the last frame

SIMPLE !

nahren

--- On Mon, 2/2/09, Shirin Awasthi  wrote:
From: Shirin Awasthi 
Subject: [gmx-users] about dumping the last frame
To: gmx-users@gromacs.org
Date: Monday, February 2, 2009, 12:00 PM

Hi. 

I have a protein model in pdb format after trjconv command.
it has 3 frames, that is 3 consecutive models of the same protein.
how do i dump only the last frame as my final model?

-- 

Shirin Awasthi
M.Tech (CSB)
Center for Computational Biology and Bioinformatics,
School of Information Technology,
Jawaharlal Nehru University,
New Delhi,
110067
INDIA.


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[gmx-users] about dumping the last frame

[Shirin Awasthi]

Hi.

I have a protein model in pdb format after trjconv command.
it has 3 frames, that is 3 consecutive models of the same protein.
how do i dump only the last frame as my final model?

-- 
Shirin Awasthi
M.Tech (CSB)
Center for Computational Biology and Bioinformatics,
School of Information Technology,
Jawaharlal Nehru University,
New Delhi,
110067
INDIA.
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[gmx-users] pdb2gmx: Bond type, Angle type, Dihedral angle type missing in topology file.

[anoop dimri]

Hi all gromacs users.

I am using gromacs v 3.3.3 on 32 bit system with suse-linux. I am working
with protein and using Gromos96 43a1 force-field. When i generate topology
file through pdb2gmx, i found that some bond types, angle types and Dihedral
angle types are missing. Some of these are related to S-S bridge and
remaining are related to HEME's Fe (intra-residual and inter-residual).
Should I fill this manually in top file ? If   anyone know why this thing is
happening, so please give me  suggestion.

Thank you.


Anoop Dimri
M.S.(Pharmacoinformatics)
NIPER Kolkata
INDIA
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Re: [gmx-users] Porcupine Plots

[Mark Abraham]

nahren manuel wrote:

Dear Gromacs Users,
 
I have done PCA of my MD , I want to visually represent the motions in 
terms of porcupine plots. I came across Dynamite (web server) for this 
purpose. But it only considers 500 frames of the xtc file.
Is there any other way how i could generate porcupine plots based on 
tools of GROMACS ?


I've never heard of such plots - perhaps you should look for pointers 
wherever you came across them in the first place?


Users on this list might help with some nuts and bolts, but first you 
need to make sure we can have access to useful information - like URLs 
and algorithm descriptions.


Mark
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Re: [gmx-users] Advice for simulating small DNA

[Mark Abraham]

Joshua Ballanco wrote:


On Feb 1, 2009, at 8:22 PM, Mark Abraham wrote:


Joshua Ballanco wrote:

On Feb 1, 2009, at 6:48 PM, Mark Abraham wrote:

Joshua Ballanco wrote:

Hi,
I'm attempting to model a system involving a small DNA 3-mer. 
Without any explicit constraints, the helix begins to come apart 
around 0.75 ns to 1 ns into the simulation.


Presumably you have a 3-mer of helices, of which at least one comes 
apart. Does a single helix in water survive? (Giving a better 
description of your simulation system would be a good idea!)
Apologies for not being more descriptive... It is a single strand of 
DNA containing 3 A-T base pairs. The system also contains a single 
Arginine residue. Simulating it in water leads to the single DNA 
strand gradually coming apart. With the DNA and water alone, the 
helix stays together much longer, but still eventually comes apart.


OK, so your model physics for DNA is intrinsically broken. Where did 
you get it?


The coordinates are from 3DNA. I'm using the terms from the G53a6 force 
field for DADE and DTHY. As for the H-bond physics, I've thus far been 
unable to find a good suggestion for how to handle these explicitly 
using Gromacs. Do you have a recommendation as to where I should be 
looking? (None of the primary literature I've looked through thus far 
seems concerned with MD of such short DNA fragments).


No, I've no idea since I don't simulate DNA.

So I'm now attempting to add restraints for the base-pair H-bonds, 
but I'm having trouble. It seems like no matter what I try, my 
system reliably explodes within the first 1 ns. My constraints look 
like this:

[ distance_restraints ]
; ai  aj  type  index type’ low up1 up2 fac
18  136 1 0 2 0.0 2.0 2.1 1.0
14  134 1 0 2 0.0 2.0 2.1 1.0
43  114 1 0 2 0.0 2.0 2.1 1.0
39  112 1 0 2 0.0 2.0 2.1 1.0
68   92 1 0 2 0.0 2.0 2.1 1.0
64   90 1 0 2 0.0 2.0 2.1 1.0
I've tried pre-equilibrating for up to 100 ps, but even that 
doesn't prevent the system from eventually exploding.


Your .mdp settings for distance restraints may also be relevant here 
- not least in setting the existence and magnitude of these restraints.

As I understand, the only relevant lines are:
constraints =  all-bonds
integrator  =  md
disre   =  simple


disre-fc and others are also relevant. See manual chapter 7.


Thanks for the pointer. I had overlooked most of the options there, 
since I'm not actually doing anything related to NMR. (That'll teach me 
to read more carefully!) Unfortunately, playing around with this, 
disre-tau, disre-weighting, and the weighting factors for each bond have 
not, so far, avoided the explosion.


OK, that's no longer surprising - distance restraints will not usefully 
fix a broken model physics.



For PME I was using:
coulombtype =  PME
rlist   =  0.55
rcoulomb=  0.55
rvdw=  0.55
fourierspacing  =  0.1375


I agree with Justin that these are very weird for normal usage.


Thanks for pointing that out. I'm relatively new with Gromacs, and 
hastily reduced these values to fix the relatively small box my system 
fits in. I doubled the short box dimension (triclinic; was --> 2.0, 2.1, 
1.1 now --> 2.0, 2.1, 2.0) and increased the radii to the (as far as I 
can tell) more recommended values:


coulombtype =  PME
rlist   =  0.9
rcoulomb=  0.9
rvdw=  0.9
fourierspacing  =  0.12


Well, that's more like it. Values for these parameters are actually 
intrinsic to the forcefield parametrization process, and one should vary 
them only with caution. This algorithmic constraint sets a minimum size 
for the simulation, of course.


When using PBC, just fitting your system into a box doesn't address the 
real issue. In a real solution this 3-mer would be close to infinite 
dilution, which can't be modeled without a serious chunk of solvent 
around it. This consideration dwarfs the algorithmic one I refer to above.


Unfortunately, even with all of these changes, I'm still getting an 
explosion (and my simulation is quite a bit slower).


Anyone can get quick random numbers - you don't even need a simulation 
package :-P There's no substitute for background literature reading, 
doing tutorials, and experimenting with preparedness for failure. :-)


Thanks again for the pointers. I'm going to try running everything with 
ffamber to see if it does a better job with the DNA (without the added 
restraints). I presume the port validated with Gromacs 3.3.1 is still 
good for 4.0?


Don't know - check out the documentation about the forcefield port - 
search the web.


Mark
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Re: [gmx-users] Advice for simulating small DNA

[Justin A. Lemkul]

Joshua Ballanco wrote:


On Feb 1, 2009, at 8:22 PM, Mark Abraham wrote:


Joshua Ballanco wrote:

On Feb 1, 2009, at 6:48 PM, Mark Abraham wrote:

Joshua Ballanco wrote:

Hi,
I'm attempting to model a system involving a small DNA 3-mer. 
Without any explicit constraints, the helix begins to come apart 
around 0.75 ns to 1 ns into the simulation.


Presumably you have a 3-mer of helices, of which at least one comes 
apart. Does a single helix in water survive? (Giving a better 
description of your simulation system would be a good idea!)
Apologies for not being more descriptive... It is a single strand of 
DNA containing 3 A-T base pairs. The system also contains a single 
Arginine residue. Simulating it in water leads to the single DNA 
strand gradually coming apart. With the DNA and water alone, the 
helix stays together much longer, but still eventually comes apart.


OK, so your model physics for DNA is intrinsically broken. Where did 
you get it?


The coordinates are from 3DNA. I'm using the terms from the G53a6 force 
field for DADE and DTHY. As for the H-bond physics, I've thus far been 
unable to find a good suggestion for how to handle these explicitly 
using Gromacs. Do you have a recommendation as to where I should be 
looking? (None of the primary literature I've looked through thus far 
seems concerned with MD of such short DNA fragments).


So I'm now attempting to add restraints for the base-pair H-bonds, 
but I'm having trouble. It seems like no matter what I try, my 
system reliably explodes within the first 1 ns. My constraints look 
like this:

[ distance_restraints ]
; ai  aj  type  index type’ low up1 up2 fac
18  136 1 0 2 0.0 2.0 2.1 1.0
14  134 1 0 2 0.0 2.0 2.1 1.0
43  114 1 0 2 0.0 2.0 2.1 1.0
39  112 1 0 2 0.0 2.0 2.1 1.0
68   92 1 0 2 0.0 2.0 2.1 1.0
64   90 1 0 2 0.0 2.0 2.1 1.0
I've tried pre-equilibrating for up to 100 ps, but even that 
doesn't prevent the system from eventually exploding.


Your .mdp settings for distance restraints may also be relevant here 
- not least in setting the existence and magnitude of these restraints.

As I understand, the only relevant lines are:
constraints =  all-bonds
integrator  =  md
disre   =  simple


disre-fc and others are also relevant. See manual chapter 7.


Thanks for the pointer. I had overlooked most of the options there, 
since I'm not actually doing anything related to NMR. (That'll teach me 
to read more carefully!) Unfortunately, playing around with this, 
disre-tau, disre-weighting, and the weighting factors for each bond have 
not, so far, avoided the explosion.



For PME I was using:
coulombtype =  PME
rlist   =  0.55
rcoulomb=  0.55
rvdw=  0.55
fourierspacing  =  0.1375


I agree with Justin that these are very weird for normal usage.


Thanks for pointing that out. I'm relatively new with Gromacs, and 
hastily reduced these values to fix the relatively small box my system 
fits in. I doubled the short box dimension (triclinic; was --> 2.0, 2.1, 
1.1 now --> 2.0, 2.1, 2.0) and increased the radii to the (as far as I 
can tell) more recommended values:


coulombtype =  PME
rlist   =  0.9
rcoulomb=  0.9
rvdw=  0.9
fourierspacing  =  0.12

Unfortunately, even with all of these changes, I'm still getting an 
explosion (and my simulation is quite a bit slower).




Read the primary literature references for Gromos96 53a6; I believe the rvdw 
parameter should be 1.4 nm to keep consistent with the parameterization scheme.


Are your box dimensions really adequate?  A standard DNA helix should be about 2 
nm wide, so your system may be seeing its periodic images if your box is only 
about 2.0 nm across its shortest dimension.  Use, for example, editconf -c -d 
1.0 to generate sufficient box dimensions.


-Justin

Thanks again for the pointers. I'm going to try running everything with 
ffamber to see if it does a better job with the DNA (without the added 
restraints). I presume the port validated with Gromacs 3.3.1 is still 
good for 4.0?


Thanks!

- Josh___
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--


Justin A. Lemkul
Graduate Research Assistant
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] Porcupine Plots

[nahren manuel]

Dear Gromacs Users,
 
I have done PCA of my MD , I want to visually represent the motions in terms of 
porcupine plots. I came across Dynamite (web server) for this purpose. But it 
only considers 500 frames of the xtc file. 
Is there any other way how i could generate porcupine plots based on tools of 
GROMACS ?
 
regards,
nahren


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Re: [gmx-users] Advice for simulating small DNA

[Joshua Ballanco]

On Feb 1, 2009, at 8:22 PM, Mark Abraham wrote:


Joshua Ballanco wrote:

On Feb 1, 2009, at 6:48 PM, Mark Abraham wrote:

Joshua Ballanco wrote:

Hi,
I'm attempting to model a system involving a small DNA 3-mer.  
Without any explicit constraints, the helix begins to come apart  
around 0.75 ns to 1 ns into the simulation.


Presumably you have a 3-mer of helices, of which at least one  
comes apart. Does a single helix in water survive? (Giving a  
better description of your simulation system would be a good idea!)
Apologies for not being more descriptive... It is a single strand  
of DNA containing 3 A-T base pairs. The system also contains a  
single Arginine residue. Simulating it in water leads to the single  
DNA strand gradually coming apart. With the DNA and water alone,  
the helix stays together much longer, but still eventually comes  
apart.


OK, so your model physics for DNA is intrinsically broken. Where did  
you get it?


The coordinates are from 3DNA. I'm using the terms from the G53a6  
force field for DADE and DTHY. As for the H-bond physics, I've thus  
far been unable to find a good suggestion for how to handle these  
explicitly using Gromacs. Do you have a recommendation as to where I  
should be looking? (None of the primary literature I've looked through  
thus far seems concerned with MD of such short DNA fragments).


So I'm now attempting to add restraints for the base-pair H- 
bonds, but I'm having trouble. It seems like no matter what I  
try, my system reliably explodes within the first 1 ns. My  
constraints look like this:

[ distance_restraints ]
; ai  aj  type  index type’ low up1 up2 fac
18  136 1 0 2 0.0 2.0 2.1 1.0
14  134 1 0 2 0.0 2.0 2.1 1.0
43  114 1 0 2 0.0 2.0 2.1 1.0
39  112 1 0 2 0.0 2.0 2.1 1.0
68   92 1 0 2 0.0 2.0 2.1 1.0
64   90 1 0 2 0.0 2.0 2.1 1.0
I've tried pre-equilibrating for up to 100 ps, but even that  
doesn't prevent the system from eventually exploding.


Your .mdp settings for distance restraints may also be relevant  
here - not least in setting the existence and magnitude of these  
restraints.

As I understand, the only relevant lines are:
constraints =  all-bonds
integrator  =  md
disre   =  simple


disre-fc and others are also relevant. See manual chapter 7.


Thanks for the pointer. I had overlooked most of the options there,  
since I'm not actually doing anything related to NMR. (That'll teach  
me to read more carefully!) Unfortunately, playing around with this,  
disre-tau, disre-weighting, and the weighting factors for each bond  
have not, so far, avoided the explosion.



For PME I was using:
coulombtype =  PME
rlist   =  0.55
rcoulomb=  0.55
rvdw=  0.55
fourierspacing  =  0.1375


I agree with Justin that these are very weird for normal usage.


Thanks for pointing that out. I'm relatively new with Gromacs, and  
hastily reduced these values to fix the relatively small box my system  
fits in. I doubled the short box dimension (triclinic; was --> 2.0,  
2.1, 1.1 now --> 2.0, 2.1, 2.0) and increased the radii to the (as far  
as I can tell) more recommended values:


coulombtype =  PME
rlist   =  0.9
rcoulomb=  0.9
rvdw=  0.9
fourierspacing  =  0.12

Unfortunately, even with all of these changes, I'm still getting an  
explosion (and my simulation is quite a bit slower).


Thanks again for the pointers. I'm going to try running everything  
with ffamber to see if it does a better job with the DNA (without the  
added restraints). I presume the port validated with Gromacs 3.3.1 is  
still good for 4.0?


Thanks!

- Josh___
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Re: [gmx-users] installation problem

[Justin A. Lemkul]

Rafael Real Guerra wrote:

Hi

Well, let’s start saying that I’m new at Linux and I’m trying to start 
on Gromacs as well.


I’ve been trying to install Gromacs 4.0 in my computer (laptop ACER 
Aspire 4530, AMD Athlon 64X2) running Mandriva 2009 and I just got stuck 
at the very beginning.


I read I need a compiler, so I downloaded GFortran 
(gcc-trunk-x86_64.tar, from 
http://gcc.gnu.org/wiki/GFortranBinaries64Linux).


 I unpacked the package using the command 
“tar xvfz gcc-trunk-x86_64.tar.gz”. A folder was created inside the 
folder I keep all the programs I am using (at “Home”).


After that, I tried to install Gromacs 4.0, and the follow screen shows up:

checking build system type… i686-pc-linux-gnuoldld

checking host system type… i686-pc-linux-gnuoldld

checking for a BSD-compatible install… /usr/bin/install -c

checking whether build environment is sane… yes

checking for a thread-save mkdir –p… /bin/mkdir -p

checking for gawk… gawk

checking whether make sets $(MAKE)… no

checking how to create a ustar tar archive… gnutar

checking for cc… no

checking for icc… no

checking for xlc… no

checking for gcc… no

configure: error: no acceptable C compiler found in $PATH

See ‘config.log’ for more details.

 

I know the problem is probably due to some error in Fortran installation 
(it should be moved to the “path”), but I have no idea how to solve it. 
What should I do?


The error has nothing to do with Fortran; the problem is quite clear - the 
configure script cannot find a C compiler.


Try typing "echo $PATH" at the command line to see which your PATH variable 
includes.  If it does not include the directories within $HOME where you are 
installing software, then add this directory to your PATH:


PATH=$PATH:$HOME/software/bin (for example)

Also, when you are finally able to install Gromacs, at least install the newest 
version (4.0.3) to get the newest bug fixes and revisions.


-Justin



Thanks

Sir Guerra



Diversão em dobro: compartilhe fotos enquanto conversa usando o Windows 
Live Messenger. 






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--


Justin A. Lemkul
Graduate Research Assistant
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] installation problem

[Rafael Real Guerra]

Hi 
Well, let’s start saying that I’m new at Linux and I’m trying to start on 
Gromacs as well. 
I’ve been trying to install Gromacs 4.0 in my computer (laptop ACER Aspire 
4530, AMD Athlon 64X2) running Mandriva 2009 and I just got stuck at the very 
beginning. 
I read I need a compiler, so I downloaded GFortran (gcc-trunk-x86_64.tar, from 
http://gcc.gnu.org/wiki/GFortranBinaries64Linux). 
 I unpacked the package using the command “tar xvfz gcc-trunk-x86_64.tar.gz”. A 
folder was created inside the folder I keep all the programs I am using (at 
“Home”). 
After that, I tried to install Gromacs 4.0, and the follow screen shows up:
checking build system type… i686-pc-linux-gnuoldld
checking host system type… i686-pc-linux-gnuoldld
checking for a BSD-compatible install… /usr/bin/install -c
checking whether build environment is sane… yes
checking for a thread-save mkdir –p… /bin/mkdir -p
checking for gawk… gawk
checking whether make sets $(MAKE)… no
checking how to create a ustar tar archive… gnutar
checking for cc… no
checking for icc… no
checking for xlc… no
checking for gcc… no
configure: error: no acceptable C compiler found in $PATH
See ‘config.log’ for more details.
 
I know the problem is probably due to some error in Fortran installation (it 
should be moved to the “path”), but I have no idea how to solve it. What should 
I do?
Thanks
Sir Guerra
_
Cansado de espaço para só 50 fotos? Conheça o Spaces, o site de relacionamentos 
com até 6,000 fotos!
http://www.amigosdomessenger.com.br___
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Re: [gmx-users] Advice for simulating small DNA

[Mark Abraham]

Joshua Ballanco wrote:

On Feb 1, 2009, at 6:48 PM, Mark Abraham wrote:


Joshua Ballanco wrote:

Hi,
I'm attempting to model a system involving a small DNA 3-mer. Without 
any explicit constraints, the helix begins to come apart around 0.75 
ns to 1 ns into the simulation.


Presumably you have a 3-mer of helices, of which at least one comes 
apart. Does a single helix in water survive? (Giving a better 
description of your simulation system would be a good idea!)


Apologies for not being more descriptive... It is a single strand of DNA 
containing 3 A-T base pairs. The system also contains a single Arginine 
residue. Simulating it in water leads to the single DNA strand gradually 
coming apart. With the DNA and water alone, the helix stays together 
much longer, but still eventually comes apart.


OK, so your model physics for DNA is intrinsically broken. Where did you 
get it?


So I'm now attempting to add restraints for the base-pair H-bonds, 
but I'm having trouble. It seems like no matter what I try, my system 
reliably explodes within the first 1 ns. My constraints look like this:

[ distance_restraints ]
; ai  aj  type  index type’ low up1 up2 fac
18  136 1 0 2 0.0 2.0 2.1 1.0
14  134 1 0 2 0.0 2.0 2.1 1.0
43  114 1 0 2 0.0 2.0 2.1 1.0
39  112 1 0 2 0.0 2.0 2.1 1.0
68   92 1 0 2 0.0 2.0 2.1 1.0
64   90 1 0 2 0.0 2.0 2.1 1.0
I've tried pre-equilibrating for up to 100 ps, but even that doesn't 
prevent the system from eventually exploding.


Your .mdp settings for distance restraints may also be relevant here - 
not least in setting the existence and magnitude of these restraints.


As I understand, the only relevant lines are:

constraints =  all-bonds
integrator  =  md
disre   =  simple


disre-fc and others are also relevant. See manual chapter 7.


For PME I was using:

coulombtype =  PME
rlist   =  0.55
rcoulomb=  0.55
rvdw=  0.55
fourierspacing  =  0.1375


I agree with Justin that these are very weird for normal usage.

Mark
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Re: [gmx-users] Advice for simulating small DNA

[Justin A. Lemkul]

Joshua Ballanco wrote:




For PME I was using:

coulombtype =  PME
rlist   =  0.55
rcoulomb=  0.55
rvdw=  0.55
fourierspacing  =  0.1375


What force field are you using?  These cut-off's seem a bit bizarre for most of 
the standard force fields distributed with Gromacs.


-Justin




If, however, I remove the distance restraints, the simulation has no 
problem.


Hmmm? This seems to contradict what you say above.


What I meant to say is that if I remove the line "disre = simple", then 
the simulation has no problem (other than the helix coming apart). With 
restraints, the system eventually explodes.


Thanks for taking a look!

Cheers,

Josh___
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Justin A. Lemkul
Graduate Research Assistant
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] Advice for simulating small DNA

[Joshua Ballanco]

On Feb 1, 2009, at 6:48 PM, Mark Abraham wrote:


Joshua Ballanco wrote:

Hi,
I'm attempting to model a system involving a small DNA 3-mer.  
Without any explicit constraints, the helix begins to come apart  
around 0.75 ns to 1 ns into the simulation.


Presumably you have a 3-mer of helices, of which at least one comes  
apart. Does a single helix in water survive? (Giving a better  
description of your simulation system would be a good idea!)


Apologies for not being more descriptive... It is a single strand of  
DNA containing 3 A-T base pairs. The system also contains a single  
Arginine residue. Simulating it in water leads to the single DNA  
strand gradually coming apart. With the DNA and water alone, the helix  
stays together much longer, but still eventually comes apart.


So I'm now attempting to add restraints for the base-pair H-bonds,  
but I'm having trouble. It seems like no matter what I try, my  
system reliably explodes within the first 1 ns. My constraints look  
like this:

[ distance_restraints ]
; ai  aj  type  index type’ low up1 up2 fac
18  136 1 0 2 0.0 2.0 2.1 1.0
14  134 1 0 2 0.0 2.0 2.1 1.0
43  114 1 0 2 0.0 2.0 2.1 1.0
39  112 1 0 2 0.0 2.0 2.1 1.0
68   92 1 0 2 0.0 2.0 2.1 1.0
64   90 1 0 2 0.0 2.0 2.1 1.0
I've tried pre-equilibrating for up to 100 ps, but even that  
doesn't prevent the system from eventually exploding.


Your .mdp settings for distance restraints may also be relevant here  
- not least in setting the existence and magnitude of these  
restraints.


As I understand, the only relevant lines are:

constraints =  all-bonds
integrator  =  md
disre   =  simple

For PME I was using:

coulombtype =  PME
rlist   =  0.55
rcoulomb=  0.55
rvdw=  0.55
fourierspacing  =  0.1375


If, however, I remove the distance restraints, the simulation has  
no problem.


Hmmm? This seems to contradict what you say above.


What I meant to say is that if I remove the line "disre = simple",  
then the simulation has no problem (other than the helix coming  
apart). With restraints, the system eventually explodes.


Thanks for taking a look!

Cheers,

Josh___
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Re: [gmx-users] Advice for simulating small DNA

[Mark Abraham]

Joshua Ballanco wrote:

Hi,

I'm attempting to model a system involving a small DNA 3-mer. Without 
any explicit constraints, the helix begins to come apart around 0.75 ns 
to 1 ns into the simulation.


Presumably you have a 3-mer of helices, of which at least one comes 
apart. Does a single helix in water survive? (Giving a better 
description of your simulation system would be a good idea!)


So I'm now attempting to add restraints for 
the base-pair H-bonds, but I'm having trouble. It seems like no matter 
what I try, my system reliably explodes within the first 1 ns. My 
constraints look like this:


[ distance_restraints ]
; ai  aj  type  index type’ low up1 up2 fac
 18  136 1 0 2 0.0 2.0 2.1 1.0
 14  134 1 0 2 0.0 2.0 2.1 1.0
 43  114 1 0 2 0.0 2.0 2.1 1.0
 39  112 1 0 2 0.0 2.0 2.1 1.0
 68   92 1 0 2 0.0 2.0 2.1 1.0
 64   90 1 0 2 0.0 2.0 2.1 1.0

I've tried pre-equilibrating for up to 100 ps, but even that doesn't 
prevent the system from eventually exploding.


Your .mdp settings for distance restraints may also be relevant here - 
not least in setting the existence and magnitude of these restraints.


If, however, I remove the 
distance restraints, the simulation has no problem.


Hmmm? This seems to contradict what you say above.

Mark

I've also tried 
instead of having distance_restraints, using a harmonic potential ([ 
bond ] with type=6), but I haven't been able to find any suggestions for 
parameterizing the harmonic potentials. I played with a few values, but 
even the harmonic potential is causing the system to explode.


I'm currently using the GROMOS96 53a6 force field with a triclinic box 
(~2, ~2, ~1,2), PME with grid spacing 1.375, two component v-rescale 
T-coupling, and no P-coupling. I'm using a 2 fs step, and I'd like to 
avoid having to change any parameters that will have an impact on run 
time (I'm less concerned about strict physical accuracy as I am with the 
ability to run ~6000 of these simulations in a reasonable amount of time).


If anyone has any advice, I'd greatly appreciate it. Thanks!

Sincerely,

Joshua Ballanco
Graduate Student
Department of Chemistry and Chemical Biology
Stevens Institute of Technology
Hoboken, NJ 07030

E-mail: jball...@gmail.com
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Re: [gmx-users] Melittin in methanol...

[Justin A. Lemkul]

sharada wrote:


Thanks for the reply.

I am sorry about the  typo mistake, it is 45a3 forcefield that I am 
working with & that I choose by giving the option 3 in pdb2gmx. So with 
PME the epsilon_r  value  has to be mentioned ?.Are the different 
forcefields 43a1,45a3 etc have to be used with different sets  of rvdw, 
rcoulomb & rlist ? In that case what would be the set of values if I am 
working with 45a3 forcefield with PME option ? How do I give correction 
term for dispersion otherwise? Are the methanol .gro and itp files that 
I am taking the right ones ?




Most of these questions can be answered by taking my earlier advice and reading 
the literature reference for the derivation of the force field.  You should not 
blindly choose a force field without understanding how it was derived and what 
it is used for, as well as how to use it.  There is no substitute for doing your 
homework.


As an aside, the 53a6 parameter set (as I suggested before) represents an 
improvement upon the 45a3 parameters; you may consider using it instead since it 
is newer and more accurate (within the criteria chosen by the developers of the 
force field).  Again, more reading will help you make in informed choice.


I see no reason to specify epsilon_r as anything other than the default (don't 
confuse it with epsilon_rf, either).  As for dispersion correction, read about 
the .mdp option DispCorr.


The methanol.gro and .itp files may or may not be what you want.  Typically the 
Gromos96 derivations are done with amino acid analogs (side chains), so the 
parameters for methanol are likely the same as for the serine side chain. 
Again, read the primary literature, and do not blindly use a topology you think 
might be appropriate.  Probably with correct parameters, the .gro file will 
suffice, provided you use an adequate equilibration scheme.


-Justin


regards,
sharada


*/-- Original Message --/*
From: "Justin A. Lemkul" 
To: "Gromacs Users' List" 
Date: Sat, 31 Jan 2009 07:35:42 -0500
Subject: Re: [gmx-users] Melittin in methanol...



sharada wrote:
 > Hello Justin,
 >
 > Thanks for the reply . I apologise for the repeat mail. The parameters
 > are for ffG43a3 forcefield. Yes I am using the default electrotatics
 > cutoff values as an initial run. I would change to PME method as you
 > say. However I was wondering If r_epsilon value equals to 66 contributes
 > to a change in the simulation or this value holds good only if reaction
 > field is on ?
 >

I have never heard of 43a3, do you mean 43a1, or perhaps 45a3? Better be 
sure
about what you're using so you get the .mdp options right. Use PME, and 
make
sure your values of rlist, rcoulomb, and rvdw are for use with that 
particular
parameter set (rvdw = 0.8 is particularly troubling, especially in the 
absence

of any dispersion correction).

With cut-off, the epsilon_r parameter is probably meaningless.

-Justin

 > sharada
 >
 >
 > */-- Original Message --/*
 > From: "Justin A. Lemkul" 
 > To: Discussion list for GROMACS users 
 > Date: Sat, 31 Jan 2009 00:42:36 -0500
 > Subject: Re: [gmx-users] Melittin in methanol...
 >
 >
 >
 > sharada wrote:
 >
 > > rlist = 0.5
 > > rcoulomb = 1.4
 > > rvdw = 0.8
 >
 > You are using cut-off electrostatics by default, so you are probably
 > getting
 > some bad artifacts (use PME instead). Also, the values of rlist,
 > rcoulomb, and
 > rvdw you are using do not correspond to those for which the Gromos96
 > force field
 > was derived. These make no sense. Refer to the original literature for
 > whichever parameter set you decided to use.
 >
 > -Justin
 >
 >
 > --
 > 
 >
 > Justin A. Lemkul
 > Graduate Research Assistant
 > Department of Biochemistry
 > Virginia Tech
 > Blacksburg, VA
 > jalemkul[at]vt.edu | (540) 231-9080
 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 > 
 > ___
 > gmx-users mailing list gmx-users@gromacs.org
 > http://www.gromacs.org/mailman/listinfo/gmx-users
 > Please search the archive at http://www.gromacs.org/search before 
posting!

 > Please don't post (un)subscribe requests to the list. Use the
 > www interface or send it to gmx-users-requ...@gromacs.org.
 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 >

--


Justin A. Lemkul
Graduate Research Assistant
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] Advice for simulating small DNA

[Joshua Ballanco]

Hi,

I'm attempting to model a system involving a small DNA 3-mer. Without  
any explicit constraints, the helix begins to come apart around 0.75  
ns to 1 ns into the simulation. So I'm now attempting to add  
restraints for the base-pair H-bonds, but I'm having trouble. It seems  
like no matter what I try, my system reliably explodes within the  
first 1 ns. My constraints look like this:


[ distance_restraints ]
; ai  aj  type  index type’ low up1 up2 fac
 18  136 1 0 2 0.0 2.0 2.1 1.0
 14  134 1 0 2 0.0 2.0 2.1 1.0
 43  114 1 0 2 0.0 2.0 2.1 1.0
 39  112 1 0 2 0.0 2.0 2.1 1.0
 68   92 1 0 2 0.0 2.0 2.1 1.0
 64   90 1 0 2 0.0 2.0 2.1 1.0

I've tried pre-equilibrating for up to 100 ps, but even that doesn't  
prevent the system from eventually exploding. If, however, I remove  
the distance restraints, the simulation has no problem. I've also  
tried instead of having distance_restraints, using a harmonic  
potential ([ bond ] with type=6), but I haven't been able to find any  
suggestions for parameterizing the harmonic potentials. I played with  
a few values, but even the harmonic potential is causing the system to  
explode.


I'm currently using the GROMOS96 53a6 force field with a triclinic box  
(~2, ~2, ~1,2), PME with grid spacing 1.375, two component v-rescale T- 
coupling, and no P-coupling. I'm using a 2 fs step, and I'd like to  
avoid having to change any parameters that will have an impact on run  
time (I'm less concerned about strict physical accuracy as I am with  
the ability to run ~6000 of these simulations in a reasonable amount  
of time).


If anyone has any advice, I'd greatly appreciate it. Thanks!

Sincerely,

Joshua Ballanco
Graduate Student
Department of Chemistry and Chemical Biology
Stevens Institute of Technology
Hoboken, NJ 07030

E-mail: jball...@gmail.com
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Re: [gmx-users] infinite polymer crystals at gromacs 4.x.x

[David van der Spoel]

Claus Valka wrote:

Hello,

back in gromacs versions 3.x.x there was the ability to simulate 
(polymer) crystals by enabling the option pbc = full in the mdp file.


That way someone was avoiding the inconsistent shifts message and was 
able to simulate infinite systems.


My question is: now in gromacs versions 4.0 and on, is this feature 
abandoned? 

The screw option, which is new, I do not think that replaces the full 
option. The full option is no longer selectable. Is there any other way? 
Or in order to use the files we were using we have to stick with older 
versions?


It should work by default in 4.0 using pbc=xyz, at least in mdrun. Let 
us know if there are problems with other tools.


Yours Sincerely,

Nikos





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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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Re: Re: [gmx-users] Melittin in methanol...

[sharada]

Thanks for the reply.
I am sorry about the  typo mistake, it is 45a3 forcefield that I am working 
with & that I choose by giving the option 3 in pdb2gmx. So with PME the 
epsilon_r  value  has to be mentioned ?.Are the different forcefields 43a1,45a3 
etc have to be used with different sets  of rvdw, rcoulomb & rlist ? In that 
case what would be the set of values if I am working with 45a3 forcefield with 
PME option ? How do I give correction term for dispersion otherwise? Are the 
methanol .gro and itp files that I am taking the right ones ? 
regards,
sharada
-- Original Message --
From: "Justin A. Lemkul" 
To: "Gromacs Users' List" 
Date: Sat, 31 Jan 2009 07:35:42 -0500
Subject: Re: [gmx-users] Melittin in methanol...
sharada wrote:
> Hello Justin,
> 
> Thanks for the reply . I apologise for the repeat mail. The parameters 
> are for ffG43a3 forcefield. Yes I am using the default electrotatics 
> cutoff values as an initial run. I would change to PME method as you 
> say. However I was wondering If r_epsilon value equals to 66 contributes 
> to a change in the simulation or this value holds good only if reaction 
> field is on ? 
> 
I have never heard of 43a3, do you mean 43a1, or perhaps 45a3? Better be sure 
about what you're using so you get the .mdp options right. Use PME, and make 
sure your values of rlist, rcoulomb, and rvdw are for use with that particular 
parameter set (rvdw = 0.8 is particularly troubling, especially in the absence 
of any dispersion correction).
With cut-off, the epsilon_r parameter is probably meaningless.
-Justin
> sharada
> 
> 
> */-- Original Message --/*
> From: "Justin A. Lemkul" 
> To: Discussion list for GROMACS users 
> Date: Sat, 31 Jan 2009 00:42:36 -0500
> Subject: Re: [gmx-users] Melittin in methanol...
> 
> 
> 
> sharada wrote:
> 
> > rlist = 0.5
> > rcoulomb = 1.4
> > rvdw = 0.8
> 
> You are using cut-off electrostatics by default, so you are probably 
> getting
> some bad artifacts (use PME instead). Also, the values of rlist, 
> rcoulomb, and
> rvdw you are using do not correspond to those for which the Gromos96 
> force field
> was derived. These make no sense. Refer to the original literature for
> whichever parameter set you decided to use.
> 
> -Justin
> 
> 
> -- 
> 
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> 
> ___
> gmx-users mailing list gmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
-- 

Justin A. Lemkul
Graduate Research Assistant
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] infinite polymer crystals at gromacs 4.x.x

[Claus Valka]

Hello,back in gromacs versions 3.x.x there was the ability to simulate 
(polymer) crystals by enabling the option pbc = full in the mdp file.That way 
someone was avoiding the inconsistent shifts message and was able to simulate 
infinite systems.My question is: now in gromacs versions 4.0 and on, is this 
feature abandoned? The screw option, which is new, I do not think that replaces 
the full option. The full option is no longer selectable. Is there any other 
way? Or in order to use the files we were using we have to stick with older 
versions?Yours Sincerely,Nikos


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Re: [gmx-users] COM motion removal

[Mark Abraham]

- Original Message -
From: priyanka srivastava 
Date: Saturday, January 31, 2009 10:20 pm
Subject: [gmx-users] COM motion removal
To: gmx-users@gromacs.org

> Dear Gromacs users!!
> 
> I have a lipid - peptide system which I simulated for 50ns. Now in the 
> beginning of the simulation the peptide was at the center of the bilayer but 
> with time the peptide moved and came very close to the edge. Now near the 
> edge it is having the interactions with the images of the lipid bilayer, 
> since pbc is on, but when I view it using ngmx then the peptide appears to be 
> lying near the edge.

If your peptide atoms can see both sides of the bilayer, then your lipid 
headgroups can also see their counterparts and you are not simulating a bilayer.

I am not sure what you think your issue is... you say the peptide "came very 
close to the edge" and then "appears to be lying near the edge".

> Is there any way by which I can write the coordinates of the images of the 
> lipid bilayer since pbc is on?Using trjconv is not helping me since it moves 
> the entire system i.e. lipid bilayer+water+peptide. So what I am looking for 
> is an option to get the images atoms so that the environment of the peptide 
> remains same and at the same time the peptide is positioned near the center 
> of the box. 

As Justin said, you should consult the other possibilities trjconv permits and 
be prepared to try a few iterates with different options to see what they do.

You can't force the "environment of the peptide" to remain the same - you are 
sampling from a heterogenous simulation environment. If it moved from the 
centre of the bilayer then postprocessing won't move it back.
 
> Also I carried out an analysis in which I calculated number of water 
> molecules around residue 1 which is actually lying very close to the edge 
> (rather outside). I think if the pbc is on then the images are taken care of 
> automatically and it will already construct image boxes around those residues 
> which are close to the edge and then perform the number of water molecules 
> around residue 1 calculation?

PBC will be taken care of. You can verify this by counting a single example 
(approximately) by hand.

Mark
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RE: [gmx-users] Re: gmx-users Digest, Vol 58, Issue 2

[Mohammed Kamal]

Saving it in the working directory should work fine. I hope that you have 
added the #include line in the right place within the topology file
Mohammed

> Date: Sun, 1 Feb 2009 16:49:17 +0530
> From: aswat...@amritapuri.amrita.edu
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Re: gmx-users Digest, Vol 58, Issue 2
> 
> Dear Mohammed,
> 
> Thanks for your reply.
> The .ITP file from the PRODRG server has saved as drg.itp and added "#include 
> "drg.itp"" line in the topology file.
> still getting the same error. 
> 
> Where should I save the drg.itp file in the present working directory or 
> share/top directory?
> 
> Thanks,
> Aswathy
> Dept. Biotechnology
> Ext. 3108
> 
> - Original Message -
> From: gmx-users-requ...@gromacs.org
> To: gmx-users@gromacs.org
> Sent: Sunday, February 1, 2009 4:30:04 PM GMT +05:30 Chennai, Kolkata, 
> Mumbai, New Delhi
> Subject: gmx-users Digest, Vol 58, Issue 2
> 
> Send gmx-users mailing list submissions to
>   gmx-users@gromacs.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
>   http://www.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
>   gmx-users-requ...@gromacs.org
> 
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>   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. RE: IN4 molecule type error (Mohammed Kamal)
> 
> 
> --
> 
> Message: 1
> Date: Sun, 1 Feb 2009 21:11:11 +1100
> From: Mohammed Kamal 
> Subject: RE: [gmx-users] IN4 molecule type error
> To: Gromacs 
> Message-ID: 
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 
> You have to include the .itp file that you have obtained from PRODRG in the 
> topology file. Be sure that you have changed the extension of the .itp file 
> that you have obtained from the PRODRG server from .ITP to .itp!!
> Mohammed
> 
> > Date: Fri, 30 Jan 2009 20:57:28 +0530
> > From: aswat...@amritapuri.amrita.edu
> > To: gmx-users@gromacs.org
> > Subject: [gmx-users] IN4 molecule type error
> > 
> > Dear Gromacs users,
> > 
> > I am a new user of gromacs. I was trying the Enzyme- Drug complex tutorial 
> > for a test run and i have ended up with following error. Please try to help 
> > me
> > 
> > 
> > creating statusfile for 1 node...
> > 
> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.90#
> > checking input for internal consistency...
> > calling /usr/bin/cpp...
> > TEST1/trp.top:12:9: error: #include expects "FILENAME" or 
> > cpp exit code: 256
> > Tried to execute: '/usr/bin/cpp  -I/usr/local/gromacs/share/top -DFLEXIBLE 
> > TEST1/trp.top > gromppVEFM2b'
> > The '/usr/bin/cpp' command is defined in the .mdp file
> > processing topology...
> > Generated 1284 of the 1485 non-bonded parameter combinations
> > Excluding 3 bonded neighbours for Protein_A 1
> > Cleaning up temporary file gromppVEFM2b
> > Fatal error: No such moleculetype IN4
> > 
> > Can you please tell me what could be the reason for this? Please help me.
> > 
> > Thanks in advance,
> > 
> > Aswathy
> > Amrita School of Biotechnology
> > Dept. Biotechnology
> > Ext. 3108
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
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> > www interface or send it to gmx-users-requ...@gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
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> Get rid of those unwanted christmas presents! Get what you want at ebay. 
> http://a.ninemsn.com.au/b.aspx?URL=http%3A%2F%2Frover%2Eebay%2Ecom%2Frover%2F1%2F705%2D10129%2D5668%2D323%2F4%3Fid%3D10&_t=763807330&_r=hotmailTAGLINES&_m=EXT
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[gmx-users] Re: gmx-users Digest, Vol 58, Issue 2

[Ms. Aswathy S]

Dear Mohammed,

Thanks for your reply.
The .ITP file from the PRODRG server has saved as drg.itp and added "#include 
"drg.itp"" line in the topology file.
still getting the same error. 

Where should I save the drg.itp file in the present working directory or 
share/top directory?

Thanks,
Aswathy
Dept. Biotechnology
Ext. 3108

- Original Message -
From: gmx-users-requ...@gromacs.org
To: gmx-users@gromacs.org
Sent: Sunday, February 1, 2009 4:30:04 PM GMT +05:30 Chennai, Kolkata, Mumbai, 
New Delhi
Subject: gmx-users Digest, Vol 58, Issue 2

Send gmx-users mailing list submissions to
gmx-users@gromacs.org

To subscribe or unsubscribe via the World Wide Web, visit
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Today's Topics:

   1. RE: IN4 molecule type error (Mohammed Kamal)


--

Message: 1
Date: Sun, 1 Feb 2009 21:11:11 +1100
From: Mohammed Kamal 
Subject: RE: [gmx-users] IN4 molecule type error
To: Gromacs 
Message-ID: 
Content-Type: text/plain; charset="iso-8859-1"


You have to include the .itp file that you have obtained from PRODRG in the 
topology file. Be sure that you have changed the extension of the .itp file 
that you have obtained from the PRODRG server from .ITP to .itp!!
Mohammed

> Date: Fri, 30 Jan 2009 20:57:28 +0530
> From: aswat...@amritapuri.amrita.edu
> To: gmx-users@gromacs.org
> Subject: [gmx-users] IN4 molecule type error
> 
> Dear Gromacs users,
> 
> I am a new user of gromacs. I was trying the Enzyme- Drug complex tutorial 
> for a test run and i have ended up with following error. Please try to help me
> 
> 
> creating statusfile for 1 node...
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.90#
> checking input for internal consistency...
> calling /usr/bin/cpp...
> TEST1/trp.top:12:9: error: #include expects "FILENAME" or 
> cpp exit code: 256
> Tried to execute: '/usr/bin/cpp  -I/usr/local/gromacs/share/top -DFLEXIBLE 
> TEST1/trp.top > gromppVEFM2b'
> The '/usr/bin/cpp' command is defined in the .mdp file
> processing topology...
> Generated 1284 of the 1485 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein_A 1
> Cleaning up temporary file gromppVEFM2b
> Fatal error: No such moleculetype IN4
> 
> Can you please tell me what could be the reason for this? Please help me.
> 
> Thanks in advance,
> 
> Aswathy
> Amrita School of Biotechnology
> Dept. Biotechnology
> Ext. 3108
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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Get rid of those unwanted christmas presents! Get what you want at ebay. 
http://a.ninemsn.com.au/b.aspx?URL=http%3A%2F%2Frover%2Eebay%2Ecom%2Frover%2F1%2F705%2D10129%2D5668%2D323%2F4%3Fid%3D10&_t=763807330&_r=hotmailTAGLINES&_m=EXT
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End of gmx-users Digest, Vol 58, Issue 2

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RE: [gmx-users] IN4 molecule type error

[Mohammed Kamal]

You have to include the .itp file that you have obtained from PRODRG in the 
topology file. Be sure that you have changed the extension of the .itp file 
that you have obtained from the PRODRG server from .ITP to .itp!!
Mohammed

> Date: Fri, 30 Jan 2009 20:57:28 +0530
> From: aswat...@amritapuri.amrita.edu
> To: gmx-users@gromacs.org
> Subject: [gmx-users] IN4 molecule type error
> 
> Dear Gromacs users,
> 
> I am a new user of gromacs. I was trying the Enzyme- Drug complex tutorial 
> for a test run and i have ended up with following error. Please try to help me
> 
> 
> creating statusfile for 1 node...
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.90#
> checking input for internal consistency...
> calling /usr/bin/cpp...
> TEST1/trp.top:12:9: error: #include expects "FILENAME" or 
> cpp exit code: 256
> Tried to execute: '/usr/bin/cpp  -I/usr/local/gromacs/share/top -DFLEXIBLE 
> TEST1/trp.top > gromppVEFM2b'
> The '/usr/bin/cpp' command is defined in the .mdp file
> processing topology...
> Generated 1284 of the 1485 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein_A 1
> Cleaning up temporary file gromppVEFM2b
> Fatal error: No such moleculetype IN4
> 
> Can you please tell me what could be the reason for this? Please help me.
> 
> Thanks in advance,
> 
> Aswathy
> Amrita School of Biotechnology
> Dept. Biotechnology
> Ext. 3108
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_
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Re: [gmx-users] genbox

[David van der Spoel]

Sunil Thapa wrote:

Respectable Mark
I am studying diffusion of oxygen in water. Can I specify the number of 
water molecules for a particular size of box. For example, I need to 
have 98 water molecules and 2 oxygen molecules in one solution. After 
that I need to increase the number of oxygen molecules and decrease the 
number of water molecules, viz, 10 oxygen molecules and 90 water molecules.
 
What i have found so far is that genbox adds the number of water 
molecules according to the size of the box. For cubical box of 1.5nm it 
adds about 110 water molecules.
 
Your help would be very helpful in this regard.


genbox -h

shows you that there is an option

genbox -maxsol

 
Sunil Kumar Thapa

Tribhuvan University, Nepal
 






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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
sp...@xray.bmc.uu.sesp...@gromacs.org   http://folding.bmc.uu.se
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[gmx-users] genbox

[Sunil Thapa]

Respectable Mark
I am studying diffusion of oxygen in water. Can I specify the number of water 
molecules for a particular size of box. For example, I need to have 98 water 
molecules and 2 oxygen molecules in one solution. After that I need to increase 
the number of oxygen molecules and decrease the number of water molecules, viz, 
10 oxygen molecules and 90 water molecules. 
 
What i have found so far is that genbox adds the number of water molecules 
according to the size of the box. For cubical box of 1.5nm it adds about 110 
water molecules. 
 
Your help would be very helpful in this regard.
 
Sunil Kumar Thapa
Tribhuvan University, Nepal
 


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