[gmx-users] DNA not wrapping around CNT in MD simulation

[majid hasan]

Dear All,

I am doing a MD simulation of dna, and cnt in water. I get a stable simulation 
in which DNA, and CNT wiggles around there positions, but they don't seem to be 
attracted towards each other. CNT starts in the middle of the box and just 
moves 
a little, and DNA starts at top right corner of the box and remains there 
throughout the simulation.

movie of .trr file is here:

http://phas.ubc.ca/~majid/Project/cntdna.mpg

My .mdp files are placed here (both .mdp files are same except for the value of 
integrator):
http://phas.ubc.ca/~majid/Project/lbfgs.mdp  (used for EM)
http://phas.ubc.ca/~majid/Project/md.mdp (used for MD)



I created cnt, and dna using following commands:
For dna: pdb2gmx -f dna.pdb -o dna.gro -p dna.top -ff select (Selected 
amber99sb, and TIP3P water model)
For cnt: g_x2top -f cnt.gro -o cnt.top -ff select -pbc   (selected amber99sb)
For mixing and solvation: genbox -cp cnt.gro -ci dna.gro -o cntdna.gro -nmol 1 
-try 20 
genbox -cp cntdna.gro -cs spc.gro -o cntdnasol.gro 

In the dna.top file, amber99sb/ions.itp, and a position restraint file was also 
included along with tip3p.itp. I mentioned it because I am not sure why would 
it 
add ions and position restraints on adding water? 

It seems that something is wrong with non-bonded interactions, but I don't 
understand what?

Thanks for your help,
Majid-- 
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Re: [gmx-users] grompp error

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Thanks Justin,

Here I pasted water.top

;
;   File 'water.top' was generated
;   By user: ndhumal (36026)
;   On host: c63
;   At date: Thu Apr 21 14:52:38 2011
;
;   This is your topology file
;   Protein
;
; Include forcefield parameters
#include "ffoplsaa.itp"

; Include water topology
;#include "spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include generic topology for ions
;#include "ions.itp"



Up to this point, you haven't defined any molecules.  You've commented out every 
topology and applied a [position_restraints] directive to a non-existent 
moleculetype.  So you've defined a force field, and then a system for which no 
molecules exist, hence the error.


-Justin


[ system ]
; Name
Protein

[ molecules ]
; Compound#mols
SOL   256

Nilesh

On Thu, April 21, 2011 8:03 pm, Justin A. Lemkul wrote:


Nilesh Dhumal wrote:


Hello,


I am trying to run a simulation for flexiable water. I use the
parameters from J. Chem. Phys. (2006),124,024503 paper and made a
spc_fw.itp file.

; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
;1   3   yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version


[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_typemasscharge   ptype  sigma  epsilon
opls_116   OW  8  9.95140-0.820   A3.165492e-01
6.50299455e-01
opls_117   HW  1  4.03200 0.410   A0.0e+00
0.0e+00


[ bondtypes ]
; ij  func   b0  kb
OWHW  11.012   443153.3808  ; J. Chem. Phys.
(2006),124,024503



[ angletypes ]
;  ijk  func   th0   cth
HW OW HW  1   113.24317.5656  ; J. Chem. Phys.
(2006),124,024503



I am geting the error for


grompp -f minim.mdp  -c water.pdb -p water.top  -o 1.tpr


error I am getting

rogram grompp, VERSION 4.0.7 Source code file: topio.c, line: 415


Fatal error:
Syntax error - File water.top, line 26
Last line read:
'[ system ]'
Invalid order for directive system


How can I fix this error?



Assemble the components of your .top in the correct order, as described
in chapter 5 of the manual.  Without seeing the contents of "water.top"
that's the best anyone can offer.

-Justin



Nilesh






--



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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Re: [gmx-users] grompp error

[Nilesh Dhumal]

Thanks Justin,

Here I pasted water.top

;
;   File 'water.top' was generated
;   By user: ndhumal (36026)
;   On host: c63
;   At date: Thu Apr 21 14:52:38 2011
;
;   This is your topology file
;   Protein
;
; Include forcefield parameters
#include "ffoplsaa.itp"

; Include water topology
;#include "spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include generic topology for ions
;#include "ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound#mols
SOL   256

Nilesh

On Thu, April 21, 2011 8:03 pm, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> Hello,
>>
>>
>> I am trying to run a simulation for flexiable water. I use the
>> parameters from J. Chem. Phys. (2006),124,024503 paper and made a
>> spc_fw.itp file.
>>
>> ; Derived from parsing of runfiles/alat.top.orig
>> [ defaults ]
>> ; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
>> ;1   3   yes 0.5 0.5
>> ; comb-rule 3 is square-root sigma, the OPLSAA version
>>
>>
>> [ atomtypes ]
>> ; full atom descriptions are available in ffoplsaa.atp
>> ; name  bond_typemasscharge   ptype  sigma  epsilon
>> opls_116   OW  8  9.95140-0.820   A3.165492e-01
>> 6.50299455e-01
>> opls_117   HW  1  4.03200 0.410   A0.0e+00
>> 0.0e+00
>>
>>
>> [ bondtypes ]
>> ; ij  func   b0  kb
>> OWHW  11.012   443153.3808  ; J. Chem. Phys.
>> (2006),124,024503
>>
>>
>>
>> [ angletypes ]
>> ;  ijk  func   th0   cth
>> HW OW HW  1   113.24317.5656  ; J. Chem. Phys.
>> (2006),124,024503
>>
>>
>>
>> I am geting the error for
>>
>>
>> grompp -f minim.mdp  -c water.pdb -p water.top  -o 1.tpr
>>
>>
>> error I am getting
>>
>> rogram grompp, VERSION 4.0.7 Source code file: topio.c, line: 415
>>
>>
>> Fatal error:
>> Syntax error - File water.top, line 26
>> Last line read:
>> '[ system ]'
>> Invalid order for directive system
>>
>>
>> How can I fix this error?
>>
>>
>
> Assemble the components of your .top in the correct order, as described
> in chapter 5 of the manual.  Without seeing the contents of "water.top"
> that's the best anyone can offer.
>
> -Justin
>
>
>> Nilesh
>>
>>
>>
>>
>>
>
> --
> 
>
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read
> http://www.gromacs.org/Support/Mailing_Lists
>
>
>


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Re: [gmx-users] grompp error

[Justin A. Lemkul]

Nilesh Dhumal wrote:

Hello,

I am trying to run a simulation for flexiable water. I use the parameters
from J. Chem. Phys. (2006),124,024503 paper and made a spc_fw.itp file.

; Derived from parsing of runfiles/alat.top.orig
 [ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
;1   3   yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

 [ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_typemasscharge   ptype  sigma  epsilon
 opls_116   OW  8  9.95140-0.820   A3.165492e-01 
6.50299455e-01

 opls_117   HW  1  4.03200 0.410   A0.0e+00  0.0e+00

[ bondtypes ]
; ij  func   b0  kb
 OWHW  11.012   443153.3808  ; J. Chem. Phys. (2006),124,024503


[ angletypes ]
;  ijk  func   th0   cth
  HW OW HW  1   113.24317.5656  ; J. Chem. Phys.
(2006),124,024503


I am geting the error for

 grompp -f minim.mdp  -c water.pdb -p water.top  -o 1.tpr


 error I am getting

rogram grompp, VERSION 4.0.7
Source code file: topio.c, line: 415

Fatal error:
Syntax error - File water.top, line 26
Last line read:
'[ system ]'
Invalid order for directive system

 How can I fix this error?



Assemble the components of your .top in the correct order, as described in 
chapter 5 of the manual.  Without seeing the contents of "water.top" that's the 
best anyone can offer.


-Justin


Nilesh






--


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] grompp error

[Nilesh Dhumal]

Hello,

I am trying to run a simulation for flexiable water. I use the parameters
from J. Chem. Phys. (2006),124,024503 paper and made a spc_fw.itp file.

; Derived from parsing of runfiles/alat.top.orig
 [ defaults ]
; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ
;1   3   yes 0.5 0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

 [ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_typemasscharge   ptype  sigma  epsilon
 opls_116   OW  8  9.95140-0.820   A3.165492e-01 
6.50299455e-01
 opls_117   HW  1  4.03200 0.410   A0.0e+00  0.0e+00

[ bondtypes ]
; ij  func   b0  kb
 OWHW  11.012   443153.3808  ; J. Chem. Phys. (2006),124,024503


[ angletypes ]
;  ijk  func   th0   cth
  HW OW HW  1   113.24317.5656  ; J. Chem. Phys.
(2006),124,024503


I am geting the error for

 grompp -f minim.mdp  -c water.pdb -p water.top  -o 1.tpr


 error I am getting

rogram grompp, VERSION 4.0.7
Source code file: topio.c, line: 415

Fatal error:
Syntax error - File water.top, line 26
Last line read:
'[ system ]'
Invalid order for directive system

 How can I fix this error?

Nilesh




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Re: [gmx-users] Improper dihedrals in Charmm FF

[Mark Abraham]

On 4/21/2011 6:54 PM, Jianguo Li wrote:

Dear all,

My molecule contains -CH=CH- fragment and I am trying to create the 
topology using Charmm FF. It seems that there is no improper dihedrals 
for -CH=CH- fragment in Charmm FF, while other FF (e.g., Amber or 
OPLS) has additional improper dihedrals terms for that fragment.

Could anybody confirm this?


That seems to be the case, but you should go and look at the primary 
sources (CHARMM parameter files and literature) to see what reasoning 
might exist.


Mark



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Re: [gmx-users] temperature effect on potential energy

[Mark Abraham]

On 4/21/2011 11:37 PM, Juliette N. wrote:



I have a quick enquiry whether temperature affects pontetial
energy
terms. Does T is accounted for to parametrize OPLS FF? Do
bonded and
nonboded energies vary with T?

Have you tried?
Try to read up on heat capacity.

Hi David,

Yes it affects potential. My question is whether this dependence is 
accounted for in parametrization (k constants in harmonic potentials..)


The generated parameters have no explicit T-dependence, so the functions 
in which they appear do not have T-dependence either.


If you want to know how a force field was parametrized, then there's no 
substitute for getting the literature and reading it.


or it affects say nb interactions in the sense that at higher T 
particles move around faster and it might be that LJ does not attract 
molecules as it would at lower T.


AFAIK, the physical interactions modelled by the LJ potential are not 
dependent on particle velocities, so why should the LJ "not attract 
molecules" at higher T? Something moving faster doesn't mean it's less 
attracted to things that it would be attracted to when traveling 
slower... gravity doesn't magically suspend for an aeroplane...


Mark



Thanks,
Jennifer N.



-- 
David van der Spoel, Ph.D., Professor of Biology

Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.se 
http://folding.bmc.uu.se
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--
Thanks,
Jennifer N.






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Re: [gmx-users] Tcoupl default setting

[Mark Abraham]

On 4/22/2011 1:51 AM, Charlie Forde wrote:

Dear All,

I had intended to perform an NPT simulation, however although I 
selected a barostat I omitted to select a thermostat, nevertheless I 
did set tc_grps= system, tau_t = 0.1 and ref_t= 300. My temperature 
appears to fluctuate around the desired 300 K. My question is, by 
setting tau_t and  ref_t has a default thermostat also been turned on 
by default 


No.

and if so which one, or have I not performed an NPT but rather an NPE 
simulation with my apparent well behaved temperature just being 
coincidental. Needless to say there is no mention of tcoupl in the 
output file.


Generate a short run that does use temperature coupling and compare the 
.log files with diff. Or, just read through the first few hundred lines 
of your .log file to see what it (doesn't) report about T-coupling.


Mark



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Re: [gmx-users] Error compiling Gromacs 4.5.4: "relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC"

[Justin A. Lemkul]

Luca Bellucci wrote:

Hi all,
I have encountered the same problem.
With this command:
./configure --with-fft=mkl --prefix=/path/gmx-4.5.3 --enable-mpi
"make mdrun" works well
 
When i used the same option with gmx 4.5.4 
 ./configure --with-fft=mkl --prefix=/path/gmx-4.5.4 --enable-mpi

"make mdrun" did not work.
The compilation reported this error:
ld: /usr/local/mpich2-1.3.2p2-install/lib/libmpich.a(allreduce.o): relocation 
R_X86_64_32 against `_2__STRING.14' can not be used when making a shared 
object; recompile with -fPIC

etc..
the problem here seems to be the use of shared or static libraries. 
I done configure command several times using the " --with-pic" and other 
combinations, however I did not resolve the problem.  Perhaps there is an 
option that I have not seen!!
Anyway I released that there is a different default behavior of the "configure" 
command.
In fact using the options reported above the configure command gives in 
configure.ac for 4.5.3 at line ~27:

AC_DISABLE_SHARED

whereas in configure.ac for 4.5.4 ther is 
AC_ENABLE_SHARED

test "$enable_mpi" = "yes" && AC_DISABLE_SHARED

When i changed these two lines in AC_DISABLE_SHARED also gmx4.5.4 is compiled. 


I think there may indeed be a problem with the build system, after all.  When I 
checked the configuration output, I saw:


...
checking whether to build shared libraries...yes
checking whether to build static libraries...yes
...

Please file a redmine issue so that this can be investigated, and fixed if 
necessary.


redmine.gromacs.org

-Justin


Luca


Pablo Englebienne wrote:

Hi all,

I'm trying to compile release 4.5.4 on a system that has been running
every release since 4.0.4 without a problem. Even 4.5.3 compiled fine
with the following configure:

LDFLAGS="-L/cvos/shared/apps/fftw/gcc/64/3.2/lib"
CPPFLAGS="-I/cvos/shared/apps/fftw/gcc/64/3.2/include" ./configure
--prefix=$HOME/software

The LDFLAGS and CPPFLAGS specify the (non-standard) location of the FFTW
libraries and headers. Configure succeeds in creating the Makefiles, but
when running make it aborts at this point:

cc  -shared  .libs/calcmu.o .libs/calcvir.o .libs/constr.o
.libs/coupling.o .libs/domdec.o .libs/domdec_box.o .libs/domdec_con.o
.libs/domdec_network.o .libs/domdec_setup.o .libs/domdec_top.o
.libs/ebin.o .libs/edsam.o .libs/ewald.o .libs/force.o .libs/forcerec.o
.libs/ghat.o .libs/init.o .libs/mdatom.o .libs/mdebin.o .libs/minimize.o
.libs/mvxvf.o .libs/ns.o .libs/nsgrid.o .libs/perf_est.o .libs/genborn.o
.libs/genborn_sse2_single.o .libs/genborn_sse2_double.o
.libs/genborn_allvsall.o .libs/genborn_allvsall_sse2_single.o
.libs/genborn_allvsall_sse2_double.o .libs/gmx_qhop_parm.o
.libs/gmx_qhop_xml.o .libs/groupcoord.o .libs/pme.o .libs/pme_pp.o
.libs/pppm.o .libs/partdec.o .libs/pull.o .libs/pullutil.o
.libs/rf_util.o .libs/shakef.o .libs/sim_util.o .libs/shellfc.o
.libs/stat.o .libs/tables.o .libs/tgroup.o .libs/tpi.o .libs/update.o
.libs/vcm.o .libs/vsite.o .libs/wall.o .libs/wnblist.o .libs/csettle.o
.libs/clincs.o .libs/qmmm.o .libs/gmx_fft.o .libs/gmx_parallel_3dfft.o
.libs/fft5d.o .libs/gmx_wallcycle.o .libs/qm_gaussian.o .libs/qm_mopac.o
.libs/qm_gamess.o .libs/gmx_fft_fftw2.o .libs/gmx_fft_fftw3.o
.libs/gmx_fft_fftpack.o .libs/gmx_fft_mkl.o .libs/qm_orca.o
.libs/mdebin_bar.o  -Wl,--rpath
-Wl,/home/penglebie/downloads/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath
-Wl,/home/penglebie/software/lib
/cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a -lxml2
-L/cvos/shared/apps/fftw/gcc/64/3.2/lib ../gmxlib/.libs/libgmx.so -lnsl
-lm  -msse2 -pthread -Wl,-soname -Wl,libmd.so.6 -o .libs/libmd.so.6.0.0
/usr/bin/ld:
/cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a(plan-many-dft-r2c.o):
relocation R_X86_64_32 against `a local symbol' can not be used when
making a shared object; recompile with -fPIC
/cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a: could not read
symbols: Bad value
collect2: ld returned 1 exit status
make[3]: *** [libmd.la] Error 1
make[3]: Leaving directory
`/home/penglebie/downloads/gromacs-4.5.4/src/mdlib'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src'
make: *** [all-recursive] Error 1

I see that recently
(http://lists.gromacs.org/pipermail/gmx-users/2011-April/059919.html)
another user encountered the same problem but this time with version
4.5.3; in my case 4.5.3 compiles fine, the only issue is with 4.5.4.

The solution is discussed in the installation instructions:

http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites


The system is running Scientific Linux 5.5.

$ uname -a

Linux ST-HPC-Main 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009
x86_64 x86_64 x86_64 GNU/Linux


I am puzzled as to why it doesn't work in 4.5.4 but did until the
previous release. Did something change in this respect?

Maybe, but the fact that this issue has come up nu

Re: [gmx-users] dna and cnt get distorted in md simulation

[majid hasan]

Okay, thank you very much. Sounds very plausibly, I will look up the .itp files 
for bonded interactions of CNT. 

Thanks,
Majid




From: Justin A. Lemkul 
To: Gromacs Users' List 
Sent: Thu, April 21, 2011 12:01:46 PM
Subject: Re: [gmx-users] dna and cnt get distorted in md simulation



majid hasan wrote:
> Okay, so here is the file that I used for both energy minimization (with 
>integrator = l-bfgs), and MD (integrator = md). Everything other than the 
>value 
>of integrator was same for both energy minimization and MD.
>  http://phas.ubc.ca/~majid/md.mdp
> 
> and here is what I see by running .trr files obtained from EM, and MD.
> 
> On running EM.trr file:
> In the beginning of simulation, DNA is very stretched i.e atoms of DNA are 
>widely separated from each other, and CNT crumples. Then, gradually DNA 
>shrinks 
>and converges onto CNT. 
>

OK, so the DNA is experiencing the charge repulsion I described earlier.  The 
CNT sounds like it does not have proper bonded interactions assigned.

> On running MD.trr file:
> CNT suddenly moves toward and DNA and one part is mixed with DNA and whole 
>structure is crumpled (similar to the final state of EM.trr simulation). Then 
>this crumpled structure wiggles around until the end of simulation.
> 

If EM is showing such weird results, then you can't really trust anything you 
see in the MD afterwards.

> 
> Yes, I ran the whole process in vacuum. I am going to do this simulation by 
>changing cutoff to shift, and see which one works better, and then I will do 
>it 
>with a solvent.
> 

There is no point in making this assessment in vacuo and then transferring it 
to 
solution.  Plain cutoffs should not be used.  Their artifacts are well-known 
and 
modern simulations should not use them.  Shifted functions have discontinuities 
at their longest cutoff and neglect electrostatic interactions beyond this 
cutoff.  Your best option in solution (especially for highly-charged molecules 
like DNA) is PME.

-Justin

> Thanks,
> Majid
> 
> *From:* Justin A. Lemkul 
> *To:* Gromacs Users' List 
> *Sent:* Thu, April 21, 2011 10:25:35 AM
> *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation
> 
> 
> 
> majid hasan wrote:
>  > first .mdp file is the original one, and modified .mdp is the one where I 
>made modifications, and I have tried both, and both lead to stable structures 
>for individual molecules, and distorted structures for combined system.
>  >
> 
> The reason I asked is that the two are very different - one is for MD and the 
>other is for EM, and in some cases, many of the options are irrelevant for 
>either process so it is somewhat hard to deduce what you're actually trying to 
>accomplish with each, especially given the differences.  It is best to only 
>post 
>the actual .mdp files you're using and a description of the output 
>corresponding 
>to each.
> 
>  > In the first .mdp file, free energy calculations are turned off, but even 
>with this file, I get huge distortions in the shape of molecules.
> 
> So, the "first" .mdp file is the one that actually specifies an MD run, not 
>EM?  Or does "first" correspond to the order of the workflow?  It might be 
>best 
>to focus on one process at a time, rather than trying to troubleshoot both EM 
>and MD with some arbitrary designators.
> 
>  > CNT, DNA atoms do form bonds in the simulation, but they lose their shapes.
> 
> Bonds don't break or form during classical MD.  Any bonds "forming" or 
>"breaking" are simply a visualization artifact since you're not reading a 
>topology into the visualization software.
> 
>  From your description, it sounds like these simulations are being conducted 
> in 
>vacuo?  I tend to suspect that is the source of the problems.  Plain cutoffs 
>for 
>electrostatics lead to nasty artifacts and the presence of a highly charged 
>molecule (DNA) that has no shielding between these charges is quite likely to 
>become very distorted due to its own intrinsic repulsion.
> 
> -Justin
> 
>  > Thank You,
>  > Majid
>  >
>  > 
>  > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
>  > *To:* Discussion list for GROMACS users >
>  > *Sent:* Thu, April 21, 2011 4:02:57 AM
>  > *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation
>  >
>  >
>  >
>  > majid hasan wrote:
>  >  > Dear All,
>  >  >
>  >  > I minimized the energy of my CNT-DNA system with l-bfgs integrator, and 
>then ran the mdrun with integrator = md. I am using a small ssDNA consisting 
>of 
>two residues only (66 atoms), and a small CNT of about 80 atoms.
>  >  > My commands are:
>  >  > For energy minimization,
>  >  >
>  >  > grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr 
>-maxwarn 20
>  >  > mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd
>

Re: [gmx-users] dna and cnt get distorted in md simulation

[Justin A. Lemkul]

majid hasan wrote:
Okay, so here is the file that I used for both energy minimization (with 
integrator = l-bfgs), and MD (integrator = md). Everything other than 
the value of integrator was same for both energy minimization and MD.

 http://phas.ubc.ca/~majid/md.mdp

and here is what I see by running .trr files obtained from EM, and MD.

On running EM.trr file:
In the beginning of simulation, DNA is very stretched i.e atoms of DNA 
are widely separated from each other, and CNT crumples. Then, gradually 
DNA shrinks and converges onto CNT. 



OK, so the DNA is experiencing the charge repulsion I described earlier.  The 
CNT sounds like it does not have proper bonded interactions assigned.



On running MD.trr file:
CNT suddenly moves toward and DNA and one part is mixed with DNA and 
whole structure is crumpled (similar to the final state of EM.trr 
simulation). Then this crumpled structure wiggles around until the end 
of simulation.




If EM is showing such weird results, then you can't really trust anything you 
see in the MD afterwards.




Yes, I ran the whole process in vacuum. I am going to do this simulation 
by changing cutoff to shift, and see which one works better, and then I 
will do it with a solvent.




There is no point in making this assessment in vacuo and then transferring it to 
solution.  Plain cutoffs should not be used.  Their artifacts are well-known and 
modern simulations should not use them.  Shifted functions have discontinuities 
at their longest cutoff and neglect electrostatic interactions beyond this 
cutoff.  Your best option in solution (especially for highly-charged molecules 
like DNA) is PME.


-Justin


Thanks,
Majid

*From:* Justin A. Lemkul 
*To:* Gromacs Users' List 
*Sent:* Thu, April 21, 2011 10:25:35 AM
*Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation



majid hasan wrote:
 > first .mdp file is the original one, and modified .mdp is the one 
where I made modifications, and I have tried both, and both lead to 
stable structures for individual molecules, and distorted structures for 
combined system.

 >

The reason I asked is that the two are very different - one is for MD 
and the other is for EM, and in some cases, many of the options are 
irrelevant for either process so it is somewhat hard to deduce what 
you're actually trying to accomplish with each, especially given the 
differences.  It is best to only post the actual .mdp files you're using 
and a description of the output corresponding to each.


 > In the first .mdp file, free energy calculations are turned off, but 
even with this file, I get huge distortions in the shape of molecules.


So, the "first" .mdp file is the one that actually specifies an MD run, 
not EM?  Or does "first" correspond to the order of the workflow?  It 
might be best to focus on one process at a time, rather than trying to 
troubleshoot both EM and MD with some arbitrary designators.


 > CNT, DNA atoms do form bonds in the simulation, but they lose their 
shapes.


Bonds don't break or form during classical MD.  Any bonds "forming" or 
"breaking" are simply a visualization artifact since you're not reading 
a topology into the visualization software.


 From your description, it sounds like these simulations are being 
conducted in vacuo?  I tend to suspect that is the source of the 
problems.  Plain cutoffs for electrostatics lead to nasty artifacts and 
the presence of a highly charged molecule (DNA) that has no shielding 
between these charges is quite likely to become very distorted due to 
its own intrinsic repulsion.


-Justin

 > Thank You,
 > Majid
 >
 > 
 > *From:* Justin A. Lemkul mailto:jalem...@vt.edu>>
 > *To:* Discussion list for GROMACS users >

 > *Sent:* Thu, April 21, 2011 4:02:57 AM
 > *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation
 >
 >
 >
 > majid hasan wrote:
 >  > Dear All,
 >  >
 >  > I minimized the energy of my CNT-DNA system with l-bfgs 
integrator, and then ran the mdrun with integrator = md. I am using a 
small ssDNA consisting of two residues only (66 atoms), and a small CNT 
of about 80 atoms.

 >  > My commands are:
 >  > For energy minimization,
 >  >
 >  > grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o 
gclb.tpr -maxwarn 20
 >  > mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g 
mdlb.log -pd

 >  >
 >  > and then I ran molecular dyamics,
 >  >
 >  > grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr 
-maxwarn 20
 >  > mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g 
mdmd.log -pd

 >  >
 >  > For individual DNA, and CNT alone, both produce reasonable 
results, where molecule stays together and jiggles around. However on 
combining the two molecules, both energy minimization and mdrun lead to 
distorted structures: bond lengt

Re: [gmx-users] dna and cnt get distorted in md simulation

[majid hasan]

Okay, so here is the file that I used for both energy minimization (with 
integrator = l-bfgs), and MD (integrator = md). Everything other than the value 
of integrator was same for both energy minimization and MD.
 http://phas.ubc.ca/~majid/md.mdp

and here is what I see by running .trr files obtained from EM, and MD.

On running EM.trr file:
In the beginning of simulation, DNA is very stretched i.e atoms of DNA are 
widely separated from each other, and CNT crumples. Then, gradually DNA shrinks 
and converges onto CNT. 

On running MD.trr file:
CNT suddenly moves toward and DNA and one part is mixed with DNA and whole 
structure is crumpled (similar to the final state of EM.trr simulation). Then 
this crumpled structure wiggles around until the end of simulation.


Yes, I ran the whole process in vacuum. I am going to do this simulation by 
changing cutoff to shift, and see which one works better, and then I will do it 
with a solvent.

Thanks,
Majid



From: Justin A. Lemkul 
To: Gromacs Users' List 
Sent: Thu, April 21, 2011 10:25:35 AM
Subject: Re: [gmx-users] dna and cnt get distorted in md simulation



majid hasan wrote:
> first .mdp file is the original one, and modified .mdp is the one where I 
> made 
>modifications, and I have tried both, and both lead to stable structures for 
>individual molecules, and distorted structures for combined system.
> 

The reason I asked is that the two are very different - one is for MD and the 
other is for EM, and in some cases, many of the options are irrelevant for 
either process so it is somewhat hard to deduce what you're actually trying to 
accomplish with each, especially given the differences.  It is best to only 
post 
the actual .mdp files you're using and a description of the output 
corresponding 
to each.

> In the first .mdp file, free energy calculations are turned off, but even 
> with 
>this file, I get huge distortions in the shape of molecules. 
>

So, the "first" .mdp file is the one that actually specifies an MD run, not EM? 
 
Or does "first" correspond to the order of the workflow?  It might be best to 
focus on one process at a time, rather than trying to troubleshoot both EM and 
MD with some arbitrary designators.

> CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. 

Bonds don't break or form during classical MD.  Any bonds "forming" or 
"breaking" are simply a visualization artifact since you're not reading a 
topology into the visualization software.

>From your description, it sounds like these simulations are being conducted in 
vacuo?  I tend to suspect that is the source of the problems.  Plain cutoffs 
for 
electrostatics lead to nasty artifacts and the presence of a highly charged 
molecule (DNA) that has no shielding between these charges is quite likely to 
become very distorted due to its own intrinsic repulsion.

-Justin

> Thank You,
> Majid
> 
> 
> *From:* Justin A. Lemkul 
> *To:* Discussion list for GROMACS users 
> *Sent:* Thu, April 21, 2011 4:02:57 AM
> *Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation
> 
> 
> 
> majid hasan wrote:
>  > Dear All,
>  >
>  > I minimized the energy of my CNT-DNA system with l-bfgs integrator, and 
> then 
>ran the mdrun with integrator = md. I am using a small ssDNA consisting of two 
>residues only (66 atoms), and a small CNT of about 80 atoms.
>  > My commands are:
>  > For energy minimization,
>  >
>  > grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr 
> -maxwarn 
>20
>  > mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd
>  >
>  > and then I ran molecular dyamics,
>  >
>  > grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 
20
>  > mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd
>  >
>  > For individual DNA, and CNT alone, both produce reasonable results, where 
>molecule stays together and jiggles around. However on combining the two 
>molecules, both energy minimization and mdrun lead to distorted structures: 
>bond 
>lengths don't remain fixed neither for CNT nor for DNA, and atoms of both 
>molecules get intertwined and produce a mess. I tried two .mdp files.
>  > I got the  first .mdp from a colleague who used it for a simple simulation 
>of CNT only (without solvent, and any other molecule) . I made few changes in 
>this file after going through manual e.g enabled free energy calculations, 
>added 
>"nsttcouple = -1" value, changed valued of "comm_mode" from Angular to Linear, 
>changed "ns_type" value from grid to simple, changed "rcoulomb" and "rvdw" 
>values from 0.9 to 1,
>  >  Both .mdp files are placed at following addresses:
>>  http://phas.ubc.ca/~majid/md.mdp  (first .mdp file)
> 
> Is this the file that has had the above modifications made to it for MD?  If 
>so, please post the actual file, not the unmodified one.
> 
>>  http://

Re: [gmx-users] dna and cnt get distorted in md simulation

[Justin A. Lemkul]

majid hasan wrote:
first .mdp file is the original one, and modified .mdp is the one where 
I made modifications, and I have tried both, and both lead to stable 
structures for individual molecules, and distorted structures for 
combined system.




The reason I asked is that the two are very different - one is for MD and the 
other is for EM, and in some cases, many of the options are irrelevant for 
either process so it is somewhat hard to deduce what you're actually trying to 
accomplish with each, especially given the differences.  It is best to only post 
the actual .mdp files you're using and a description of the output corresponding 
to each.


In the first .mdp file, free energy calculations are turned off, but 
even with this file, I get huge distortions in the shape of molecules. 



So, the "first" .mdp file is the one that actually specifies an MD run, not EM? 
 Or does "first" correspond to the order of the workflow?  It might be best to 
focus on one process at a time, rather than trying to troubleshoot both EM and 
MD with some arbitrary designators.


CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. 



Bonds don't break or form during classical MD.  Any bonds "forming" or 
"breaking" are simply a visualization artifact since you're not reading a 
topology into the visualization software.


From your description, it sounds like these simulations are being conducted in 
vacuo?  I tend to suspect that is the source of the problems.  Plain cutoffs for 
electrostatics lead to nasty artifacts and the presence of a highly charged 
molecule (DNA) that has no shielding between these charges is quite likely to 
become very distorted due to its own intrinsic repulsion.


-Justin


Thank You,
Majid


*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Thu, April 21, 2011 4:02:57 AM
*Subject:* Re: [gmx-users] dna and cnt get distorted in md simulation



majid hasan wrote:
 > Dear All,
 >
 > I minimized the energy of my CNT-DNA system with l-bfgs integrator, 
and then ran the mdrun with integrator = md. I am using a small ssDNA 
consisting of two residues only (66 atoms), and a small CNT of about 80 
atoms.

 > My commands are:
 > For energy minimization,
 >
 > grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr 
-maxwarn 20

 > mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd
 >
 > and then I ran molecular dyamics,
 >
 > grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr 
-maxwarn 20

 > mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd
 >
 > For individual DNA, and CNT alone, both produce reasonable results, 
where molecule stays together and jiggles around. However on combining 
the two molecules, both energy minimization and mdrun lead to distorted 
structures: bond lengths don't remain fixed neither for CNT nor for DNA, 
and atoms of both molecules get intertwined and produce a mess. I tried 
two .mdp files.
 > I got the  first .mdp from a colleague who used it for a simple 
simulation of CNT only (without solvent, and any other molecule) . I 
made few changes in this file after going through manual e.g enabled 
free energy calculations, added "nsttcouple = -1" value, changed valued 
of "comm_mode" from Angular to Linear, changed "ns_type" value from grid 
to simple, changed "rcoulomb" and "rvdw" values from 0.9 to 1,

 >  Both .mdp files are placed at following addresses:

 http://phas.ubc.ca/~majid/md.mdp  (first .mdp file)


Is this the file that has had the above modifications made to it for 
MD?  If so, please post the actual file, not the unmodified one.



 http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file)

 >
 > It seems to me that problem might be related to non-bonded 
interaction because this is the significant difference between one and 
two molecule system. Any help would be much appreciated.


Why are you employing the free energy code?  It seems to me this could 
be the source of your problems.  Each molecule alone is fine, but then 
by decoupling van der Waals and Coulombic interactions between them, you 
could be getting instability.


Turn off the free energy options and see if you get stable trajectories.

-Justin

 > Thanks,
 > Majid
 >

-- 

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] dna and cnt get distorted in md simulation

[majid hasan]

first .mdp file is the original one, and modified .mdp is the one where I made 
modifications, and I have tried both, and both lead to stable structures for 
individual molecules, and distorted structures for combined system.

In the first .mdp file, free energy calculations are turned off, but even with 
this file, I get huge distortions in the shape of molecules. 

CNT, DNA atoms do form bonds in the simulation, but they lose their shapes. 

Thank You,
Majid




From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Thu, April 21, 2011 4:02:57 AM
Subject: Re: [gmx-users] dna and cnt get distorted in md simulation



majid hasan wrote:
> Dear All,
> 
> I minimized the energy of my CNT-DNA system with l-bfgs integrator, and then 
>ran the mdrun with integrator = md. I am using a small ssDNA consisting of two 
>residues only (66 atoms), and a small CNT of about 80 atoms. 
>
> My commands are:
> For energy minimization,
> 
> grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr -maxwarn 
20
> mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd
> 
> and then I ran molecular dyamics,
> 
> grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20
> mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd
> 
> For individual DNA, and CNT alone, both produce reasonable results, where 
>molecule stays together and jiggles around. However on combining the two 
>molecules, both energy minimization and mdrun lead to distorted structures: 
>bond 
>lengths don't remain fixed neither for CNT nor for DNA, and atoms of both 
>molecules get intertwined and produce a mess. I tried two .mdp files. 
>
> I got the  first .mdp from a colleague who used it for a simple simulation of 
>CNT only (without solvent, and any other molecule) . I made few changes in 
>this 
>file after going through manual e.g enabled free energy calculations, added 
>"nsttcouple = -1" value, changed valued of "comm_mode" from Angular to Linear, 
>changed "ns_type" value from grid to simple, changed "rcoulomb" and "rvdw" 
>values from 0.9 to 1,
>   Both .mdp files are placed at following addresses:
> http://phas.ubc.ca/~majid/md.mdp   (first .mdp file)

Is this the file that has had the above modifications made to it for MD?  If 
so, 
please post the actual file, not the unmodified one.

> http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file)
> 
> It seems to me that problem might be related to non-bonded interaction 
> because 
>this is the significant difference between one and two molecule system. Any 
>help 
>would be much appreciated. 
>

Why are you employing the free energy code?  It seems to me this could be the 
source of your problems.  Each molecule alone is fine, but then by decoupling 
van der Waals and Coulombic interactions between them, you could be getting 
instability.

Turn off the free energy options and see if you get stable trajectories.

-Justin

> Thanks,
> Majid
> 

-- 

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] Tcoupl default setting‏

[Charlie Forde]

Dear All,

I had intended to perform an NPT simulation, however
although I selected a barostat I omitted to select a thermostat,
nevertheless I did set tc_grps= system, tau_t = 0.1 and ref_t= 300. My
temperature appears to fluctuate around the desired 300 K. My question
is, by setting tau_t and  ref_t has a default thermostat also been
turned on by default and if so which one, or have I not performed an
NPT but rather an NPE simulation with my apparent well behaved
temperature just being coincidental. Needless to say there is no
mention of tcoupl in the output file.

Regards

Charlie.


Apologies for possible double posting
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[gmx-users] Tcoupl default setting

[Charlie Forde]

Dear All,

I had intended to perform an NPT simulation, however although I selected a 
barostat I omitted to select a thermostat, nevertheless I did set tc_grps= 
system, tau_t = 0.1 and ref_t= 300. My temperature appears to fluctuate around 
the desired 300 K. My question is, by setting tau_t and  ref_t has a default 
thermostat also been turned on by default and if so which one, or have I not 
performed an NPT but rather an NPE simulation with my apparent well behaved 
temperature just being coincidental. Needless to say there is no mention of 
tcoupl in the output file.

Regards

Charlie.
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Re: [gmx-users] binding_affinity

[Justin A. Lemkul]

shahid nayeem wrote:

Hi Justin
Before trying for my system I am trying to learn running these
simulation with the help of your tutorial. The only change I made is
that I applied pull_code for 2nm movement only in order to save time.
Thereafter, with trjconv I generated all 200 conf.gro. when I run your
perl script it does gives an oitput of summary_distance.dat. It has
one column of conf.gro number but no distance. Where I am wrong.


I don't know exactly, but the script runs 500 iterations of each calculation, so 
you may have 200 lines of content then 300 incomplete lines, unless you've 
properly modified the script.


-Justin


Shahid Nayeem

On Tue, Apr 19, 2011 at 6:20 PM, Justin A. Lemkul  wrote:


Justin A. Lemkul wrote:


shahid nayeem wrote:

Hi Justin
Thanks a lot. What is the purpose of adding 100mM NaCl. Is it
mimicking physiological condition.

More of a hybrid of physiological and in vitro conditions.  Please see the
referenced paper for more details.


...and again, please don't necessarily conclude that just because someone
did this for a tutorial that you should inherently be doing it for your
system.  The tutorial is but one example of a workflow, derived from my own
specific work. Construct a model that is most appropriate to your purposes.

-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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--


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] binding_affinity

[shahid nayeem]

Hi Justin
Before trying for my system I am trying to learn running these
simulation with the help of your tutorial. The only change I made is
that I applied pull_code for 2nm movement only in order to save time.
Thereafter, with trjconv I generated all 200 conf.gro. when I run your
perl script it does gives an oitput of summary_distance.dat. It has
one column of conf.gro number but no distance. Where I am wrong.
Shahid Nayeem

On Tue, Apr 19, 2011 at 6:20 PM, Justin A. Lemkul  wrote:
>
>
> Justin A. Lemkul wrote:
>>
>>
>> shahid nayeem wrote:
>>>
>>> Hi Justin
>>> Thanks a lot. What is the purpose of adding 100mM NaCl. Is it
>>> mimicking physiological condition.
>>
>> More of a hybrid of physiological and in vitro conditions.  Please see the
>> referenced paper for more details.
>>
>
> ...and again, please don't necessarily conclude that just because someone
> did this for a tutorial that you should inherently be doing it for your
> system.  The tutorial is but one example of a workflow, derived from my own
> specific work. Construct a model that is most appropriate to your purposes.
>
> -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] temperature effect on potential energy

[Juliette N.]

>
>> I have a quick enquiry whether temperature affects pontetial energy
>> terms. Does T is accounted for to parametrize OPLS FF? Do bonded and
>> nonboded energies vary with T?
>>
>>  Have you tried?
> Try to read up on heat capacity.
>
> Hi David,

Yes it affects potential. My question is whether this dependence is
accounted for in parametrization (k constants in harmonic potentials..) or
it affects say nb interactions in the sense that at higher T particles move
around faster and it might be that LJ does not attract molecules as it would
at lower T.

>
>> Thanks,
>> Jennifer N.
>>
>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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>



-- 
Thanks,
Jennifer N.
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Re: [gmx-users] temperature effect on potential energy

[David van der Spoel]

On 2011-04-21 15.24, Juliette N. wrote:


Hello,

I have a quick enquiry whether temperature affects pontetial energy
terms. Does T is accounted for to parametrize OPLS FF? Do bonded and
nonboded energies vary with T?


Have you tried?
Try to read up on heat capacity.



Thanks,
Jennifer N.




--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] temperature effect on potential energy

[Juliette N.]

Hello,

I have a quick enquiry whether temperature affects pontetial energy terms.
Does T is accounted for to parametrize OPLS FF? Do bonded and nonboded
energies vary with T?


Thanks,
Jennifer N.
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Re: [gmx-users] cholesterol

[Mark Abraham]

On 4/21/2011 8:05 PM, Preeti Gupta wrote:

Hi All,

I am new user of gromacs and i want to simulate cholesterol + DOPC as 
my final year project.
firstly i tried gromacs with cholesterol, for which i have downloaded 
cholesterol pdb and itp file from gromacs site by Monika Hoeltje.
i m getting the following error- Residue 'CHOL' not found in residue 
topology database.


... which you need if only if you want to use pdb2gmx on a structure file.

I tried PRODRG for generating cholesterol topology file and coordinate 
file, but still i got the error-

invalid directive of atomtype.


So you've got some file format wrong...

can someone give me charmm residue topology file for cholesterol or 
with some solution.


I think you will profit from doing some tutorial material and looking at 
the examples in chapter 5 of the manual.


Mark



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Re: [gmx-users] dna and cnt get distorted in md simulation

[Justin A. Lemkul]

majid hasan wrote:

Dear All,

I minimized the energy of my CNT-DNA system with l-bfgs integrator, and 
then ran the mdrun with integrator = md. I am using a small ssDNA 
consisting of two residues only (66 atoms), and a small CNT of about 80 
atoms. 


My commands are:
For energy minimization,

grompp -f lbfgs.mdp -po mdoutlb.mdp -c gc.gro -p gc.top -o gclb.tpr 
-maxwarn 20

mdrun -s gclb.tpr -o gclb.trr -c gcoutlb.gro -e gclb.edr -g mdlb.log -pd

and then I ran molecular dyamics,

grompp -f md.mdp -po mdoutmd.mdp -c gc.gro -p gc.top -o gcmd.tpr -maxwarn 20
mdrun -s gcmd.tpr -o gcmd.trr -c gcoutmd.gro -e gcmd.edr -g mdmd.log -pd

For individual DNA, and CNT alone, both produce reasonable results, 
where molecule stays together and jiggles around. However on combining 
the two molecules, both energy minimization and mdrun lead to 
distorted structures: bond lengths don't remain fixed neither for CNT 
nor for DNA, and atoms of both molecules get intertwined and produce a 
mess. I tried two .mdp files. 

I got the  first .mdp from a colleague who used it for a 
simple simulation of CNT only (without solvent, and any other molecule) 
. I made few changes in this file after going through manual e.g enabled 
free energy calculations, added "nsttcouple = -1" value, changed valued 
of "comm_mode" from Angular to Linear, changed "ns_type" value from grid 
to simple, changed "rcoulomb" and "rvdw" values from 0.9 to 1,
 
 Both .mdp files are placed at following addresses:

http://phas.ubc.ca/~majid/md.mdp   (first .mdp file)


Is this the file that has had the above modifications made to it for MD?  If so, 
please post the actual file, not the unmodified one.



http://phas.ubc.ca/~majid/lbfgs.mdp (modified .mdp file)

It seems to me that problem might be related to non-bonded interaction 
because this is the significant difference between one and two molecule 
system. Any help would be much appreciated. 



Why are you employing the free energy code?  It seems to me this could be the 
source of your problems.  Each molecule alone is fine, but then by decoupling 
van der Waals and Coulombic interactions between them, you could be getting 
instability.


Turn off the free energy options and see if you get stable trajectories.

-Justin


Thanks,
Majid



--


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] Error compiling Gromacs 4.5.4: "relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC"

[Luca Bellucci]

Hi all,
I have encountered the same problem.
With this command:
./configure --with-fft=mkl --prefix=/path/gmx-4.5.3 --enable-mpi
"make mdrun" works well
 
When i used the same option with gmx 4.5.4 
 ./configure --with-fft=mkl --prefix=/path/gmx-4.5.4 --enable-mpi
"make mdrun" did not work.
The compilation reported this error:
ld: /usr/local/mpich2-1.3.2p2-install/lib/libmpich.a(allreduce.o): relocation 
R_X86_64_32 against `_2__STRING.14' can not be used when making a shared 
object; recompile with -fPIC
etc..
the problem here seems to be the use of shared or static libraries. 
I done configure command several times using the " --with-pic" and other 
combinations, however I did not resolve the problem.  Perhaps there is an 
option that I have not seen!!
Anyway I released that there is a different default behavior of the "configure" 
command.
In fact using the options reported above the configure command gives in 
configure.ac for 4.5.3 at line ~27:
AC_DISABLE_SHARED

whereas in configure.ac for 4.5.4 ther is 
AC_ENABLE_SHARED
test "$enable_mpi" = "yes" && AC_DISABLE_SHARED

When i changed these two lines in AC_DISABLE_SHARED also gmx4.5.4 is compiled. 
Luca

> Pablo Englebienne wrote:
> > Hi all,
> > 
> > I'm trying to compile release 4.5.4 on a system that has been running
> > every release since 4.0.4 without a problem. Even 4.5.3 compiled fine
> > with the following configure:
> > 
> > LDFLAGS="-L/cvos/shared/apps/fftw/gcc/64/3.2/lib"
> > CPPFLAGS="-I/cvos/shared/apps/fftw/gcc/64/3.2/include" ./configure
> > --prefix=$HOME/software
> > 
> > The LDFLAGS and CPPFLAGS specify the (non-standard) location of the FFTW
> > libraries and headers. Configure succeeds in creating the Makefiles, but
> > when running make it aborts at this point:
> > 
> > cc  -shared  .libs/calcmu.o .libs/calcvir.o .libs/constr.o
> > .libs/coupling.o .libs/domdec.o .libs/domdec_box.o .libs/domdec_con.o
> > .libs/domdec_network.o .libs/domdec_setup.o .libs/domdec_top.o
> > .libs/ebin.o .libs/edsam.o .libs/ewald.o .libs/force.o .libs/forcerec.o
> > .libs/ghat.o .libs/init.o .libs/mdatom.o .libs/mdebin.o .libs/minimize.o
> > .libs/mvxvf.o .libs/ns.o .libs/nsgrid.o .libs/perf_est.o .libs/genborn.o
> > .libs/genborn_sse2_single.o .libs/genborn_sse2_double.o
> > .libs/genborn_allvsall.o .libs/genborn_allvsall_sse2_single.o
> > .libs/genborn_allvsall_sse2_double.o .libs/gmx_qhop_parm.o
> > .libs/gmx_qhop_xml.o .libs/groupcoord.o .libs/pme.o .libs/pme_pp.o
> > .libs/pppm.o .libs/partdec.o .libs/pull.o .libs/pullutil.o
> > .libs/rf_util.o .libs/shakef.o .libs/sim_util.o .libs/shellfc.o
> > .libs/stat.o .libs/tables.o .libs/tgroup.o .libs/tpi.o .libs/update.o
> > .libs/vcm.o .libs/vsite.o .libs/wall.o .libs/wnblist.o .libs/csettle.o
> > .libs/clincs.o .libs/qmmm.o .libs/gmx_fft.o .libs/gmx_parallel_3dfft.o
> > .libs/fft5d.o .libs/gmx_wallcycle.o .libs/qm_gaussian.o .libs/qm_mopac.o
> > .libs/qm_gamess.o .libs/gmx_fft_fftw2.o .libs/gmx_fft_fftw3.o
> > .libs/gmx_fft_fftpack.o .libs/gmx_fft_mkl.o .libs/qm_orca.o
> > .libs/mdebin_bar.o  -Wl,--rpath
> > -Wl,/home/penglebie/downloads/gromacs-4.5.4/src/gmxlib/.libs -Wl,--rpath
> > -Wl,/home/penglebie/software/lib
> > /cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a -lxml2
> > -L/cvos/shared/apps/fftw/gcc/64/3.2/lib ../gmxlib/.libs/libgmx.so -lnsl
> > -lm  -msse2 -pthread -Wl,-soname -Wl,libmd.so.6 -o .libs/libmd.so.6.0.0
> > /usr/bin/ld:
> > /cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a(plan-many-dft-r2c.o):
> > relocation R_X86_64_32 against `a local symbol' can not be used when
> > making a shared object; recompile with -fPIC
> > /cvos/shared/apps/fftw/gcc/64/3.2/lib/libfftw3f.a: could not read
> > symbols: Bad value
> > collect2: ld returned 1 exit status
> > make[3]: *** [libmd.la] Error 1
> > make[3]: Leaving directory
> > `/home/penglebie/downloads/gromacs-4.5.4/src/mdlib'
> > make[2]: *** [all-recursive] Error 1
> > make[2]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src'
> > make[1]: *** [all] Error 2
> > make[1]: Leaving directory `/home/penglebie/downloads/gromacs-4.5.4/src'
> > make: *** [all-recursive] Error 1
> > 
> > I see that recently
> > (http://lists.gromacs.org/pipermail/gmx-users/2011-April/059919.html)
> > another user encountered the same problem but this time with version
> > 4.5.3; in my case 4.5.3 compiles fine, the only issue is with 4.5.4.
> 
> The solution is discussed in the installation instructions:
> 
> http://www.gromacs.org/Downloads/Installation_Instructions#Prerequisites
> 
> > The system is running Scientific Linux 5.5.
> > 
> > $ uname -a
> > 
> > Linux ST-HPC-Main 2.6.18-128.7.1.el5 #1 SMP Mon Aug 24 08:12:52 EDT 2009
> > x86_64 x86_64 x86_64 GNU/Linux
> > 
> > 
> > I am puzzled as to why it doesn't work in 4.5.4 but did until the
> > previous release. Did something change in this respect?
> 
> Maybe, but the fact that this issue has come up numerous times in several
> versions suggests not.  As for why 4.5.3 works and 4.5.4 doesn't, I can

[gmx-users] cholesterol

[Preeti Gupta]

Hi All,

I am new user of gromacs and i want to simulate cholesterol + DOPC as my final 
year project.
firstly i tried gromacs with cholesterol, for which i have downloaded 
cholesterol pdb and itp file from gromacs site by Monika Hoeltje. 

i m getting the following error- Residue 'CHOL' not found in residue topology 
database.
I tried PRODRG for generating cholesterol topology file and coordinate file, 
but 
still i got the error-
invalid directive of atomtype.

can someone give me charmm residue topology file for cholesterol or with some 
solution.

Thanks in advance.-- 
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[gmx-users] Improper dihedrals in Charmm FF

[Jianguo Li]

Dear all,

My molecule contains -CH=CH- fragment and I am trying to create the topology 
using Charmm FF. It seems that there is no improper dihedrals for -CH=CH- 
fragment in Charmm FF, while other FF (e.g., Amber or OPLS) has additional 
improper dihedrals terms for that fragment. 

Could anybody confirm this?
Thanks very much!

Cheers,
Jianguo-- 
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[gmx-users] Re: gmx-users Digest, Vol 84, Issue 177

[Gerrit Groenhof]

> 
>   4. PYP Connection (Taylor Kaplan)


Are the connections between the chromophore and cysteine there? You can check 
this by scanning your topology file for the indices of the sulphur and C1 atom 
in the [ bonds ] section. 

You can use the specbond the attach the chromophore to the protein. THis so far 
always worked for us.

hope it helps,

Gerrit



> Message: 4
> Date: Thu, 21 Apr 2011 00:48:07 -0700 (PDT)
> From: Taylor Kaplan 
> Subject: [gmx-users] PYP Connection
> To: Discussion list for GROMACS users 
> Message-ID: <441414.8442...@web36601.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi Rama,
> 
>I was looking at the tdb files for the amber03 force field ( I didn't 
> change anything, i just read with the cat command ), anyways I didn't see 
> anything written in the tdb -n or -c terminal files. After reading the 
> gromacs manual on topology files, it said that residue connection types and 
> such are specified through the tdb file. I'm only guessing that since the 
> chromophore isn't an amino acid that it may have a different connection 
> deviating from the traditional -n or -c terminals. So I was wondering if the 
> amber force field was using the .tdb files that comes standard with gromacs 
> ,... which I'm pretty sure lacks the type of connection that pyp makes with 
> the protein. So to fix this problem, do we need to make or modify the .tdb 
> file for the chromophore, or is the .tdb file of no concern? 
> 
> Thanks,
> 
> Taylor
> 
> --- On Wed, 4/20/11, Ramachandran G  wrote:
> 
> From: Ramachandran G 
> Subject: Re: [gmx-users] PYP chromophore force field
> To: "Peter C. Lai" 
> Cc: "gmx-users@gromacs.org" 
> Date: Wednesday, April 20, 2011, 5:12 PM
> 
> 
> Yes, you are right, the chromophore(p-coumaric acid) is covalently bonded to 
> the Sulphur(S) atom of the Cys-69 residue.
> But I specified the covalent bond in my topology.
> 
> [ bonds]
>  C   +SG
> 
> [ angles ]
> 
>   OC   +SG   
>  CA1   C   +SG   
>   C  +SG   +CB  
> 
> [ dihedrals ]
>   O C  +SG+CB
>  CA1C  +SG+CB
>  HA2   CA1   C   +SG
>  CA2   CA1   C   +SG
>   C   +SG  +CB   +CA
> 
>   C   +SG  +CB   +HB1
>   C   +SG  +CB   +HB2
> 
> After doing pdb2gmx, i got the right structure. But the chromophore flies 
> away after minimising. 
> 
> 
> Thanks
> Rama
> 
> On Wed, Apr 20, 2011 at 4:57 PM, Peter C. Lai  wrote:
> 
> Isn't the chromophore supposed to be covalently bonded to the protein?
> 
> My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al
> 
> 1994 and van Beeumen et al 1993: "This small 125-residue protein contains a
> 
> p-coumaric acid chromophore that is covalently bound to the protein backbone
> 
> via a thiol-ester cysteine linkage Cys-69"...
> 
> 
> 
> Maybe you forgot to specify a covalent bond in your topology...
> 
> 
> 
> On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote:
> 
>> Hi gromacs users,
> 
>>  I am working on Photo active yellow protein.
> 
>> 
> 
>> Although i successfully build the force field and patched the 
>> chromophore to the protein.
> 
>> After energy minimizing the protein, the chromophore flies away separately. 
>> I don't know whether i am missing anything?
> 
>> Please help.
> 
>> Rama
> 
>> 
> 
>> 
> 
> 
> 
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> Peter C. Lai | University of Alabama-Birmingham
> 
> Programmer/Analyst   | BEC 257
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> Genetics, Div. of Research   | 1150 10th Avenue South
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[gmx-users] PYP Connection

[Taylor Kaplan]

Hi Rama,

   I was looking at the tdb files for the amber03 force field ( I didn't change 
anything, i just read with the cat command ), anyways I didn't see anything 
written in the tdb -n or -c terminal files. After reading the gromacs manual on 
topology files, it said that residue connection types and such are specified 
through the tdb file. I'm only guessing that since the chromophore isn't an 
amino acid that it may have a different connection deviating from the 
traditional -n or -c terminals. So I was wondering if the amber force field was 
using the .tdb files that comes standard with gromacs ,... which I'm pretty 
sure lacks the type of connection that pyp makes with the protein. So to fix 
this problem, do we need to make or modify the .tdb file for the chromophore, 
or is the .tdb file of no concern? 

Thanks,

Taylor

--- On Wed, 4/20/11, Ramachandran G  wrote:

From: Ramachandran G 
Subject: Re: [gmx-users] PYP chromophore force field
To: "Peter C. Lai" 
Cc: "gmx-users@gromacs.org" 
Date: Wednesday, April 20, 2011, 5:12 PM


Yes, you are right, the chromophore(p-coumaric acid) is covalently bonded to 
the Sulphur(S) atom of the Cys-69 residue.
But I specified the covalent bond in my topology.

[ bonds]
 C   +SG

[ angles ]

  O    C   +SG   
 CA1   C   +SG   
  C  +SG   +CB  

[ dihedrals ]
  O C  +SG    +CB
 CA1    C  +SG    +CB
 HA2   CA1   C   +SG
 CA2   CA1   C   +SG
  C   +SG  +CB   +CA

  C   +SG  +CB   +HB1
  C   +SG  +CB   +HB2

After doing pdb2gmx, i got the right structure. But the chromophore flies away 
after minimising. 


Thanks
Rama

On Wed, Apr 20, 2011 at 4:57 PM, Peter C. Lai  wrote:

Isn't the chromophore supposed to be covalently bonded to the protein?

My cursory search shows Vengris et al 2004 in Biophys. J. citing Baca et al

1994 and van Beeumen et al 1993: "This small 125-residue protein contains a

p-coumaric acid chromophore that is covalently bound to the protein backbone

via a thiol-ester cysteine linkage Cys-69"...



Maybe you forgot to specify a covalent bond in your topology...



On 2011-04-20 06:46:54PM -0500, Ramachandran G wrote:

> Hi gromacs users,

>      I am working on Photo active yellow protein.

>

>     Although i successfully build the force field and patched the chromophore 
> to the protein.

> After energy minimizing the protein, the chromophore flies away separately. I 
> don't know whether i am missing anything?

> Please help.

> Rama

>

>



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===

Peter C. Lai                 | University of Alabama-Birmingham

Programmer/Analyst           | BEC 257

Genetics, Div. of Research   | 1150 10th Avenue South

p...@uab.edu                  | Birmingham AL 35294-4461

(205) 690-0808               |

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