date:20111114

Re: [gmx-users] Time unit issue with g_anaeig

2011-11-14 Thread Mark Abraham


On 14/11/2011 5:46 PM, Kei Sit wrote:


Hi all,

I'm new to gromacs so I hope I haven't done something wrong that is 
extremely simple. I have recently been using gromacs to analyse an MD 
trajectory using g_covar and g_anaeig. I have output saved to the 
trajectory every ps and I currently have a trajectory with 49000 
frames (49ns).


I initiate g_anaeig with this command:

g_anaeig --v eigenvec.trr  --f 1-21.trr --s protein.pdb --eig 
eigenval.xvg --proj projection.xvg --xvgr --first 1 --last 8


While this is being executed I see this:

Reading frame 1000 time 100.00

which continues increasing as more frames are read.

When I go to visualise projection.xvg, the time scale is in ps 
(natural as the default value is in ps) but it only shows 4900ps and 
not 49000ps.


My issue is  this, why is the time constantly 10 times smaller than 
the number of frames that are being read? Am I not entering something 
correctly which fixes this?





What does gmxcheck have to say about your trajectory files?

Mark
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[gmx-users] orca and Segmentation fault

2011-11-14 Thread xi zhao

dear sir : 
 I installed gromacs-orca for qm/mm
./configure --without-qmmm-orca --with--qmmm-gaussian --enable-mpi 
make 
make install 
MPI is lam-mpi
 
when run mdrun , the error 
" Back Off! I just backed up md.log to ./#md.log.12#
Getting Loaded...
Reading file pyp.tpr, VERSION 4.5.1 (single precision)
Loaded with Money
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
there we go!
there we go!
there we go!
there we go!
there we go!
there we go!
there we go!
Layer 0
nr of QM atoms 22
QMlevel: B3LYP/3-21G
orca initialised...
[localhost:17937] *** Process received signal ***
[localhost:17939] *** Process received signal ***
[localhost:17937] Signal: Segmentation fault (11)
[localhost:17937] Signal code: Address not mapped (1)
[localhost:17937] Failing at address: 0x10
[localhost:17940] *** Process received signal ***
[localhost:17939] Signal: Segmentation fault (11)
[localhost:17939] Signal code: Address not mapped (1)
[localhost:17939] Failing at address: 0x10
[localhost:17936] *** Process received signal ***
[localhost:17936] Signal: Segmentation fault (11)
[localhost:17936] Signal code: Address not mapped (1)
[localhost:17936] Failing at address: 0x10
[localhost:17934] *** Process received signal ***
[localhost:17938] *** Process received signal ***
[localhost:17934] Signal: Segmentation fault (11)
[localhost:17934] Signal code: Address not mapped (1)
[localhost:17934] Failing at address: 0x10
[localhost:17940] Signal: Segmentation fault (11)
[localhost:17940] Signal code: Address not mapped (1)
[localhost:17940] Failing at address: 0x10
[localhost:17938] Signal: Segmentation fault (11)
[localhost:17938] Signal code: Address not mapped (1)
[localhost:17938] Failing at address: 0x10
[localhost:17939] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17939] [ 1] mdrun_dd [0x534a93]
[localhost:17939] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
[localhost:17939] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
[localhost:17939] [ 4] mdrun_dd(main+0xe69) [0x43d619]
[localhost:17939] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
[0x35c4f1c3fb]
[localhost:17939] [ 6] mdrun_dd [0x41bcfa]
[localhost:17939] *** End of error message ***
[localhost:17936] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17936] [ 1] mdrun_dd [0x534a93]
[localhost:17936] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
[localhost:17936] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
[localhost:17936] [ 4] mdrun_dd(main+0xe69) [0x43d619]
[localhost:17936] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
[0x35c4f1c3fb]
[localhost:17936] [ 6] mdrun_dd [0x41bcfa]
[localhost:17936] *** End of error message ***
[localhost:17940] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17940] [ 1] mdrun_dd [0x534a93]
[localhost:17940] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
[localhost:17940] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
[localhost:17940] [ 4] mdrun_dd(main+0xe69) [0x43d619]
[localhost:17940] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
[0x35c4f1c3fb]
[localhost:17940] [ 6] mdrun_dd [0x41bcfa]
[localhost:17940] *** End of error message ***
there we go!
[localhost:17935] *** Process received signal ***
[localhost:17935] Signal: Segmentation fault (11)
[localhost:17935] Signal code: Address not mapped (1)
[localhost:17935] Failing at address: 0x10
[localhost:17935] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17935] [ 1] mdrun_dd [0x534a93]
[localhost:17935] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
[localhost:17935] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
[localhost:17935] [ 4] mdrun_dd(main+0xe69) [0x43d619]
[localhost:17935] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
[0x35c4f1c3fb]
[localhost:17935] [ 6] mdrun_dd [0x41bcfa]
[localhost:17935] *** End of error message ***
[localhost:17934] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17934] [ 1] mdrun_dd [0x534a93]
[localhost:17934] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
[localhost:17934] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
[localhost:17934] [ 4] mdrun_dd(main+0xe69) [0x43d619]
[localhost:17934] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
[0x35c4f1c3fb]
[localhost:17934] [ 6] mdrun_dd [0x41bcfa]
[localhost:17934] *** End of error message ***
[localhost:17937] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17937] [ 1] mdrun_dd [0x534a93]
[localhost:17937] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
[localhost:17937] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
[localhost:17937] [ 4] mdrun_dd(main+0xe69) [0x43d619]
[localhost:17937] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
[0x35c4f1c3fb]
[localhost:17937] [ 6] mdrun_dd [0x41bcfa]
[localhost:17937] *** End of error message ***
[localhost:17938] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17938] [ 1] mdrun_dd [0x534a93]
[localhost:17938] [ 2] m

[gmx-users] Problem about simulation at high temperature and ratio of sencondary stuctures

2011-11-14 Thread 蕭翔駿

Hi Gromacs users,

 

I am using GROMACS (ver4.5.3) to run molecular dynamics (MD) simulation.
However during my simulation runs, I encountered some problems as stated
below:

 

1. In NPT condition, the box size undergoes changes, especially at high
temperature simulations. However, during semisotropic pressure coupling, the
box size changed dramatically at x/y or z direction. That made the box thin
and long or flat. On the top of that, it caused fatal error in the runs and
the simulations stopped running altogether. Can this situation be prevented
? If so, how can it be done?

 

2. I have found that command “g_helix” can calculate helix properties.
Nevertheless, my concern is with beta sheet. I did not find any tools in
Gromacs that can calculate the ratio of beta sheet from MD trajectories. Do
you have any recommendations?

 

I'd appreciate any help you can give me on this and am looking forward to
hearing from you soon.

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[gmx-users] Atomtype 'CR' not found

2011-11-14 Thread radhika jaswal

Hiii All...

I want to do steepest descent energy minimization for molecule 
Bromobenzisoxazolone Barretin, I have all the required files like.itp and .gro. 
Also, changed force field from ffG43a1 to ffgmx but no use. Same error of 
Atomtype 'CR' not found, is coming again n again. Please suggest me possible 
corrections.

Thanks in advance
Radhika
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Re: [gmx-users] orca and Segmentation fault

2011-11-14 Thread Christoph Riplinger


Dear xi zhao,

In your case GMX is applying threading and thus not only a single QM job 
is requested, but eight. You should run mdrun with -nt 1. Then GMX uses 
only one single CPU and ORCA is called only once (but can be used in 
parallel).

Hope that helps,
Christoph

On 11/14/2011 10:34 AM, xi zhao wrote:

dear sir :
 I installed gromacs-orca for qm/mm
./configure --without-qmmm-orca --with--qmmm-gaussian --enable-mpi
make
make install
MPI is lam-mpi
when run mdrun , the error
" Back Off! I just backed up md.log to ./#md.log.12#
Getting Loaded...
Reading file pyp.tpr, VERSION 4.5.1 (single precision)
Loaded with Money
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
there we go!
there we go!
there we go!
there we go!
there we go!
there we go!
there we go!
Layer 0
nr of QM atoms 22
QMlevel: B3LYP/3-21G
orca initialised...
[localhost:17937] *** Process received signal ***
[localhost:17939] *** Process received signal ***
[localhost:17937] Signal: Segmentation fault (11)
[localhost:17937] Signal code: Address not mapped (1)
[localhost:17937] Failing at address: 0x10
[localhost:17940] *** Process received signal ***
[localhost:17939] Signal: Segmentation fault (11)
[localhost:17939] Signal code: Address not mapped (1)
[localhost:17939] Failing at address: 0x10
[localhost:17936] *** Process received signal ***
[localhost:17936] Signal: Segmentation fault (11)
[localhost:17936] Signal code: Address not mapped (1)
[localhost:17936] Failing at address: 0x10
[localhost:17934] *** Process received signal ***
[localhost:17938] *** Process received signal ***
[localhost:17934] Signal: Segmentation fault (11)
[localhost:17934] Signal code: Address not mapped (1)
[localhost:17934] Failing at address: 0x10
[localhost:17940] Signal: Segmentation fault (11)
[localhost:17940] Signal code: Address not mapped (1)
[localhost:17940] Failing at address: 0x10
[localhost:17938] Signal: Segmentation fault (11)
[localhost:17938] Signal code: Address not mapped (1)
[localhost:17938] Failing at address: 0x10
[localhost:17939] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17939] [ 1] mdrun_dd [0x534a93]
[localhost:17939] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
[localhost:17939] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
[localhost:17939] [ 4] mdrun_dd(main+0xe69) [0x43d619]
[localhost:17939] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
[0x35c4f1c3fb]

[localhost:17939] [ 6] mdrun_dd [0x41bcfa]
[localhost:17939] *** End of error message ***
[localhost:17936] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17936] [ 1] mdrun_dd [0x534a93]
[localhost:17936] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
[localhost:17936] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
[localhost:17936] [ 4] mdrun_dd(main+0xe69) [0x43d619]
[localhost:17936] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
[0x35c4f1c3fb]

[localhost:17936] [ 6] mdrun_dd [0x41bcfa]
[localhost:17936] *** End of error message ***
[localhost:17940] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17940] [ 1] mdrun_dd [0x534a93]
[localhost:17940] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
[localhost:17940] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
[localhost:17940] [ 4] mdrun_dd(main+0xe69) [0x43d619]
[localhost:17940] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
[0x35c4f1c3fb]

[localhost:17940] [ 6] mdrun_dd [0x41bcfa]
[localhost:17940] *** End of error message ***
there we go!
[localhost:17935] *** Process received signal ***
[localhost:17935] Signal: Segmentation fault (11)
[localhost:17935] Signal code: Address not mapped (1)
[localhost:17935] Failing at address: 0x10
[localhost:17935] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17935] [ 1] mdrun_dd [0x534a93]
[localhost:17935] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
[localhost:17935] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
[localhost:17935] [ 4] mdrun_dd(main+0xe69) [0x43d619]
[localhost:17935] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
[0x35c4f1c3fb]

[localhost:17935] [ 6] mdrun_dd [0x41bcfa]
[localhost:17935] *** End of error message ***
[localhost:17934] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17934] [ 1] mdrun_dd [0x534a93]
[localhost:17934] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
[localhost:17934] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
[localhost:17934] [ 4] mdrun_dd(main+0xe69) [0x43d619]
[localhost:17934] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
[0x35c4f1c3fb]

[localhost:17934] [ 6] mdrun_dd [0x41bcfa]
[localhost:17934] *** End of error message ***
[localhost:17937] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17937] [ 1] mdrun_dd [0x534a93]
[localhost:17937] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
[localhost:17937] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
[localhost:17937] [ 4] mdrun_dd(main+0xe69) [0x43d

[gmx-users] Could g_order be used to calculate the order parameters for the two bonds C1'-H1', C3'-H3' in DNA?

2011-11-14 Thread jnsong

Dear all,

Recently, I have performed simulation on a B-DNA using gromacs, and I
want to use g_order in gromacs to get the order parameters for the bonds
C1'-H1', C3'-H3'. Is it possible to obtain order parameters for these
two bonds with g_order? If possible, Would you please tell me the
correct way to get order parameters for C1'-H1', C3'-H3'?

Thank you very much!

jnsong
 

P.S. I just had a try using g_order, the process is as follows:

-

> a C1'

Found 24 atoms with name C1'

 11 C1' :24 atoms

> a H1' 

Found 24 atoms with name H1'

 12 H1' :24 atoms

> del 0-10

Removed group 0 'System'
Removed group 1 'DNA'
Removed group 2 'K'
Removed group 3 'CL'
Removed group 4 'Water'
Removed group 5 'SOL'
Removed group 6 'non-Water'
Removed group 7 'Ion'
Removed group 8 'K'
Removed group 9 'CL'
Removed group 10 'Water_and_ions'

> q
-


through this I get index.ndx for C1'-H1' and 

then I perform: 

> g_order -f md.xtc -s md.tpr -n index.ndx -o

and I get order.xvg, but there are no order parameters in order.xvg and 

the contents of order.xvg are as follows:

--
# This file was created Thu Nov 10 20:00:06 2011
# by the following command:
# g_order -f md.xtc -n index.ndx -s md.tpr -o -ob 
#
# g_order is part of G R O M A C S:
#
# GROup of MAchos and Cynical Suckers
#
@title "Order tensor diagonal elements"
@xaxis  label "Atom"
@yaxis  label "S"
@TYPE xy
--



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Re: [gmx-users] orca and Segmentation fault

2011-11-14 Thread xi zhao



./configure --without-qmmm-orca --without--qmmm-gaussian --enable-mpi 
make 
make install 
I installed  gromacs with Parallel  mode,  is not threading. when I run  " 
mpirun -np 1 mdrun_dd -v -s pyp.tpr&" or mdrun_dd -nt 1 -v -s pyp.tpr
it still"
Back Off! I just backed up md.log to ./#md.log.20#
Getting Loaded...
Reading file pyp.tpr, VERSION 4.5.1 (single precision)
Loaded with Money
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 22
QMlevel: B3LYP/3-21G
orca initialised...
Back Off! I just backed up traj.trr to ./#traj.trr.1#
Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
Back Off! I just backed up ener.edr to ./#ener.edr.2#
starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water'
500 steps,  0.5 ps.
Calling 'orca pyp.inp >> pyp.out'
Error : multiplicity (Mult:=2*S+1) is zero
---
Program mdrun_dd, VERSION 4.5.1
Source code file: qm_orca.c, line: 393
Fatal error:
Call to 'orca pyp.inp >> pyp.out' failed
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
"The Carpenter Goes Bang Bang" (The Breeders)
Halting program mdrun_dd
gcq#129: "The Carpenter Goes Bang Bang" (The Breeders)
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD 
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--
--
mpirun has exited due to process rank 0 with PID 18080 on
node localhost.localdomai exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here)."


--- 11年11月14日，周一, Christoph Riplinger  写道：


发件人: Christoph Riplinger 
主题: Re: [gmx-users] orca and Segmentation fault
收件人: "Discussion list for GROMACS users" 
日期: 2011年11月14日,周一,下午6:51



Dear xi zhao,

In your case GMX is applying threading and thus not only a single QM job is 
requested, but eight. You should run mdrun with -nt 1. Then GMX uses only one 
single CPU and ORCA is called only once (but can be used in parallel).
Hope that helps,
Christoph

On 11/14/2011 10:34 AM, xi zhao wrote: 





dear sir : 
 I installed gromacs-orca for qm/mm
./configure --without-qmmm-orca --without--qmmm-gaussian --enable-mpi 
make 
make install 
MPI is lam-mpi
 
when run mdrun , the error 
" Back Off! I just backed up md.log to ./#md.log.12#
Getting Loaded...
Reading file pyp.tpr, VERSION 4.5.1 (single precision)
Loaded with Money
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
QM/MM calculation requested.
there we go!
there we go!
there we go!
there we go!
there we go!
there we go!
there we go!
Layer 0
nr of QM atoms 22
QMlevel: B3LYP/3-21G
orca initialised...
[localhost:17937] *** Process received signal ***
[localhost:17939] *** Process received signal ***
[localhost:17937] Signal: Segmentation fault (11)
[localhost:17937] Signal code: Address not mapped (1)
[localhost:17937] Failing at address: 0x10
[localhost:17940] *** Process received signal ***
[localhost:17939] Signal: Segmentation fault (11)
[localhost:17939] Signal code: Address not mapped (1)
[localhost:17939] Failing at address: 0x10
[localhost:17936] *** Process received signal ***
[localhost:17936] Signal: Segmentation fault (11)
[localhost:17936] Signal code: Address not mapped (1)
[localhost:17936] Failing at address: 0x10
[localhost:17934] *** Process received signal ***
[localhost:17938] *** Process received signal ***
[localhost:17934] Signal: Segmentation fault (11)
[localhost:17934] Signal code: Address not mapped (1)
[localhost:17934] Failing at address: 0x10
[localhost:17940] Signal: Segmentation fault (11)
[localhost:17940] Signal code: Address not mapped (1)
[localhost:17940] Failing at address: 0x10
[localhost:17938] Signal: Segmentation fault (11)
[localhost:17938] Signal code: Address not mapped (1)
[localhost:17938] Failing at address: 0x10
[localhost:17939] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17939] [ 1] mdrun_dd [0x534a93]
[localhost:17939] [ 2] mdrun_dd(init_QMMMrec+0x3e1) [0x5353f1]
[localhost:17939] [ 3] mdrun_dd(mdrunner+0x112c) [0x43200c]
[localhost:17939] [ 4] mdrun_dd(main+0xe69) [0x43d619]
[localhost:17939] [ 5] /lib64/tls/libc.so.6(__libc_start_main+0xdb) 
[0x35c4f1c3fb]
[localhost:17939] [ 6] mdrun_dd [0x41bcfa]
[localhost:17939] *** End of error message ***
[localhost:17936] [ 0] /lib64/tls/libpthread.so.0 [0x35c5a0c430]
[localhost:17936] [ 1] mdrun_dd [0x534a93]

RE: [gmx-users] Potential Energy Landscape

2011-11-14 Thread Natalie Stephenson



From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: 21 October 2011 13:25
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Potential Energy Landscape

Natalie Stephenson wrote:
>> Hi Justin (and gmx-users),
>>
>> I've been looking into using g_sham for the free energy landscapes, however
>> I'm not sure what variables I should plot ... could I just use the g_energy
>> (potential) outputs to produce the energy landscape??  Other examples I've
>> seen using g_sham have done quite in depth eigenvector projections before
>> plotting them using g_sham.
>>
>
>The free energy of potential energy is probably not a meaningful quantity ;)
>
>> What inputs would I require in order to determine how loading rate an
>> increased loading rate on the simulation would change the force results?
>>
>> I know I'm probably being completely dumb but my use of maths has been
>> sporadic to say the least in the last 7 years ... so getting back into it is
>> proving more confusing!
>>
>
>You haven't provided a lot of detail about what you're doing, what you've
>measured, or what you hope to achieve.  In general, one plots two variables 
>(one
>on each axis), and g_sham calculates a free energy based simply on the
>probability of occurrence of these values.  For instance, for protein folding
>experiments, often the RMSD relative to the known structure is one variable, 
>and
>something else like native contacts or hydrogen bonds is plotted as the other
>variable.  The free energy surface is then generated as a function of
>intramolecular association and similarity to a known structure.
>
>-Justin
>

Sorry it's taken so long to reply to this one, experimental issues dragged my 
focus!
I have performed force pulling experiments on a protein with both Gromacs MD 
simulations and experimentally with AFM.  The problem I'm facing with the data 
is the difference between the loading rates of the two approaches.  For the MDS 
the loading rate is around 10 N/s, whereas the AFM experiments have a much 
lower loading rate of 1 x 10^-8 N/s. 

I was told at a conference I attended that there was a way of constructing a 
'potential energy landscape' which would be able to use this to remove the 
loading rate differences. However, I did not get a chance to find out how this 
was possible.  I understand how g_sham works, however, I'm not sure what - in 
this case - the input would be in order to construct such a 'potential energy 
landscape'. Any insight into how I would be able to create this ... or any 
other ideas on how I would be able to somehow relate the simulation output to 
experimental data dispite the loading rate differences would be GREATLY 
appreciated!!

Thanks once again!!
Natalie

> Natalie
>
>  Natalie Stephenson, B.Sc PhD
> Research Associate
>
> Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN
> x65816 
>
>  From: gmx-users-boun...@gromacs.org
> [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul
> [jalem...@vt.edu] Sent: 12 October 2011 18:22 To: Discussion list for GROMACS
> users Subject: Re: [gmx-users] Potential Energy Landscape
>
> Natalie Stephenson wrote:
>> I was recently told in passing that it would be possible to construct a
>> 'potential energy landscape' from the simulations I have performed. This
>> way I could remove any loading rate differences between simulations and
>> experimental force experiments I've been performing ... however I cannot
>> find anywhere in which this is mentioned.
>>
>> The only thing close I could find that was close was the free energy
>> landscape using g_anaeig under the Dihedral PCA
>> (http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA?highlight=dihedral+pca
>>
>> )
>>  however, I'm not sure this is what I'm looking for.
>>
>> Does anyone know where I would be able to find out / read more about how to
>> create potential energy landscapes from my simulation outputs?
>>
>
> g_sham produces free energy landscapes for any variables plotted against one
> another.
>
> -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] Atomtype 'CR' not found

2011-11-14 Thread Mark Abraham


On 14/11/2011 9:08 PM, radhika jaswal wrote:

Hiii All...

I want to do steepest descent energy minimization for molecule 
Bromobenzisoxazolone Barretin, I have all the required files like.itp 
and .gro. Also, changed force field from ffG43a1 to ffgmx but no use. 
Same error of Atomtype 'CR' not found, is coming again n again. Please 
suggest me possible corrections.




Having the files is just not enough - they've got to have contents that 
make sense in the context of the force field. You need to find a force 
field whose atom types include suitable models for this compound. The 
.itp needs to be generated for the force field. So wherever you sourced 
these files determines the force field.


Mark
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[gmx-users] Re: orca and Segmentation fault (xi zhao)

2011-11-14 Thread Gerrit Groenhof



THe error message is clear: your spin multiplicity is 0, which is 
impossible.
Please make sure you understand the basics of electronic structure 
theory. To test this, you can run the QM system only in stand along QM 
package.


gerrit


2. Re: orca and Segmentation fault (xi zhao)
3. RE: Potential Energy Landscape (Natalie Stephenson)


-

./configure --without-qmmm-orca --without--qmmm-gaussian --enable-mpi
make
make install
I installedÂ  gromacs with ParallelÂ Â mode,Â  is not threading. when I run Â " mpirun 
-np 1 mdrun_dd -v -s pyp.tpr&" or mdrun_dd -nt 1Â -v -s pyp.tpr
it still"
Back Off! I just backed up md.log to ./#md.log.20#
Getting Loaded...
Reading file pyp.tpr, VERSION 4.5.1 (single precision)
Loaded with Money
QM/MM calculation requested.
there we go!
Layer 0
nr of QM atoms 22
QMlevel: B3LYP/3-21G
orca initialised...
Back Off! I just backed up traj.trr to ./#traj.trr.1#
Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
Back Off! I just backed up ener.edr to ./#ener.edr.2#
starting mdrun 'PHOTOACTIVE YELLOW PROTEIN in water'
500 steps,Â Â Â Â Â  0.5 ps.
Calling 'orca pyp.inp>>  pyp.out'
Error : multiplicity (Mult:=2*S+1) is zero
---
Program mdrun_dd, VERSION 4.5.1
Source code file: qm_orca.c, line: 393
Fatal error:
Call to 'orca pyp.inp>>  pyp.out' failed
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
"The Carpenter Goes Bang Bang" (The Breeders)
Halting program mdrun_dd
gcq#129: "The Carpenter Goes Bang Bang" (The Breeders)
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--
--
mpirun has exited due to process rank 0 with PID 18080 on
node localhost.localdomai exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here)."


--- 11å¹´11æœˆ14æ—¥ï¼Œå‘¨ä¸€, Christoph Riplinger  
å†™é�“ï¼š


å�‘ä»¶äºº: Christoph Riplinger
ä¸»é¢˜: Re: [gmx-users] orca and Segmentation fault
æ”¶ä»¶äºº: "Discussion list for GROMACS users"
æ—¥æœŸ: 2011å¹´11æœˆ14æ—¥,å‘¨ä¸€,ä¸‹å�ˆ6:51





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Re: [gmx-users] Problem about simulation at high temperature and ratio of sencondary stuctures

2011-11-14 Thread Mark Abraham


On 14/11/2011 8:33 PM, ??? wrote:


Hi Gromacs users,

I am using GROMACS (ver4.5.3) to run molecular dynamics (MD) 
simulation. However during my simulation runs, I encountered some 
problems as stated below:


1. In NPT condition, the box size undergoes changes, especially at 
high temperature simulations. However, during semisotropic pressure 
coupling, the box size changed dramatically at x/y or z direction. 
That made the box thin and long or flat. On the top of that, it caused 
fatal error in the runs and the simulations stopped running 
altogether. Can this situation be prevented ? If so, how can it be done?




Perhaps the models in your systems are intrinsically unsuited to these 
simulation conditions. To my knowledge, no common biomolecular force 
field has been parametrized against high-temperature NPT data. Under 
these conditions, the assumptions about safe sizes for integration time 
steps need not hold, so you may find smaller steps are more stable.


2. I have found that command "g_helix" can calculate helix properties. 
Nevertheless, my concern is with beta sheet. I did not find any tools 
in Gromacs that can calculate the ratio of beta sheet from MD 
trajectories. Do you have any recommendations?




do_dssp with old-style DSSP installed is the only GROMACS offering that 
can address this. Check out manual section 7.4 for overviews of tools.


Mark
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[gmx-users] mpirun with remd

2011-11-14 Thread 杜波

dear teacher,
when i do remd ,i use the commond :
mpirun n8,8,8,8,9,10,15,16,16,20,20,22 -np 24
/export/software/bin/mdrun_mpi_4.5.5 -multidir ./0/  ./1/ ./2/ ./3/ ./4/
./5/ ./6/ ./7/ ./8/ ./9/ ./10/ ./11/ -replex 1000 -nice 0 -s pmma.tpr -o md
-c after_md -pd -table table.xvg -tableb table.xvg -v >& log1 &

node16:
PID USER  PR  NI  VIRT  RES  SHR S %CPU %MEMTIME+  COMMAND
14411 KD16   0 51528 3552 2728 R 67.6  0.1   6:47.63 mdrun_mpi_4.5.5
14409 KD15   0 51528 3612 2788 S 25.9  0.1   1:22.06 mdrun_mpi_4.5.5
14408 KD15   0 51516 3396 2580 S 22.2  0.1   1:10.81 mdrun_mpi_4.5.5
14410 KD15   0 51508 3212 2408 S 20.6  0.1   1:07.22 mdrun_mpi_4.5.5

and we have 4 cpus on this node16 & there are no other program except the
system's:,
why only  one %CPU of thread (14411 ) is big ?

thanks!
regards,
Bo Du
Department of Polymer Science and Engineering,
School of Chemical Engineering and technology,
Tianjin University, Weijin Road 92, Nankai District 300072,
Tianjin City P. R. China
Tel/Fax: +86-22-27404303
E-mail: 2008d...@gmail.com
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Re: [gmx-users] mpirun with remd

2011-11-14 Thread Mark Abraham


On 15/11/2011 12:22 AM, 杜波 wrote:

dear teacher,
when i do remd ,i use the commond :
mpirun n8,8,8,8,9,10,15,16,16,20,20,22 -np 24 
/export/software/bin/mdrun_mpi_4.5.5 -multidir ./0/ ./1/ ./2/ ./3/ 
./4/ ./5/ ./6/ ./7/ ./8/ ./9/ ./10/ ./11/ -replex 1000 -nice 0 -s 
pmma.tpr -o md -c after_md -pd -table table.xvg -tableb table.xvg -v 
>& log1 &


node16:
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
14411 KD 16 0 51528 3552 2728 R 67.6 0.1 6:47.63 mdrun_mpi_4.5.5
14409 KD 15 0 51528 3612 2788 S 25.9 0.1 1:22.06 mdrun_mpi_4.5.5
14408 KD 15 0 51516 3396 2580 S 22.2 0.1 1:10.81 mdrun_mpi_4.5.5
14410 KD 15 0 51508 3212 2408 S 20.6 0.1 1:07.22 mdrun_mpi_4.5.5

and we have 4 cpus on this node16 & there are no other program except 
the system's:,

why only one %CPU of thread (14411 ) is big ?


We don't really know enough to say. We don't know that this percentage 
is a valid metric on your system or that your mpirun invocation is 
valid. Set up a run that should take a few minutes and compare the time 
taken in serial with one or two processors, and with REMD systems of 
various numbers of replicas. Now you can start to track down what, if 
any, problem is occurring.


Mark

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Re: [gmx-users] GROMACS/ORCA QMMM

2011-11-14 Thread Christoph Riplinger


Dear Jose,

I tried oniom which stopped for me either (although without a segfault). 
Have you tried "QMMMscheme normal"?


Christoph

On 11/11/2011 05:53 PM, Jose Tusell wrote:

Dear GROMACS users,

I'm trying to run a QM-MM optimization.  I solvate my protein and add
ions then I do a classical optimization (just GROMACS).  After that I
run grompp with the following minim.mdp file (just showing qmmm
options):

QMMM= yes
QMMM-grps   = Other
QMmethod= RHF
QMbasis = 3-21G
QMMMscheme  = Oniom
QMcharge= -1
QMmult  = 1
SH  = no

This creates the *.tpr file that use to run mdrun.  I use the
following *.ORCAINFO file:

!PAL8 Quick-DFT VerySlowConv
%scf
   Maxiter 300
end
%pal nprocs 8
end

The ORCA run quickly converges but after that mdrun run stops with a
segmentation fault.  Am I missing something in all of this?  Any help
would be greatly appreciated.

Thanks

Jose Tusell

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[gmx-users] The equilibrium before REMD simulations

2011-11-14 Thread ÏéÇ« ¿×

Dear GMX users,
  I am puzzled about some technical details regarding to the REMD simulation 
and eager for your generous help.
  With the purpose to explore the additional conformational space of the 
protein, I want to employ the REMD method in Gromacs. However, I noticed that 
in almost all of the papers about REMD, a short equilibrium with NPT or NVT was 
performed for each replica respectively before the final REMD run. But i think 
the initial structure of each replica for REMD run is thus different due to the 
respective equilibrium and may somewhat go against the concept of replicas 
which i suppose should have same initial structures while with different 
temperatures. So my question is whether we should or not perform the NVT or 
NPT equilibrium before REMD simulations BTW and why? BTW, i also want to know 
which ensemble should we use in REMD because some papers use NPT while others 
use NVT.  
 Thanks in advance!
 Best regards!
 Xiangqian Kong
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Re: [gmx-users] The equilibrium before REMD simulations

2011-11-14 Thread Justin A. Lemkul




ÏéÇ« ¿× wrote:

Dear GMX users, I am puzzled about some technical details regarding to the
REMD simulation and eager for your generous help. With the purpose to explore
the additional conformational space of the protein, I want to employ the REMD
method in Gromacs. However, I noticed that in almost all of the papers about
REMD, a short equilibrium with NPT or NVT was performed for each replica
respectively before the final REMD run. But i think the initial structure of
each replica for REMD run is thus different due to the respective equilibrium
and may somewhat go against the concept of replicas which i suppose should
have same initial structures while with different temperatures. So my
question is whether we should or not perform the NVT or NPT equilibrium
before REMD simulations BTW and why? BTW, i also want to know which ensemble


Yes, always equilibrate.  Otherwise, your systems will almost certainly not be 
stable.  Position restraints are typically applied to the solute of interest 
during the initial equilibration, making initial differences almost insignificant.


should we use in REMD because some papers use NPT while others use NVT. 


Pressure coupling algorithms frequently break down at high temperature, so NVT 
is often used.


-Justin

--


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


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[gmx-users] Units of Buckingham potential

2011-11-14 Thread xiaojing gong

Hi dear all,
 For Buckingham potential， there is three parameters A B C
 In GMX, the units of A B C is the kJ/mol, nm, kJ/mol*nm^6， am I right?

Best
XJ
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Re: [gmx-users] Units of Buckingham potential

2011-11-14 Thread Mark Abraham


On 15/11/2011 2:00 AM, xiaojing gong wrote:

Hi dear all,
For Buckingham potential， there is three parameters A B C
In GMX, the units of A B C is the kJ/mol, nm, kJ/mol*nm^6， am I right?


Manual section 2.2 defines the units, and 4.1.2 defines the functional form.

Mark
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Re: [gmx-users] The equilibrium before REMD simulations

2011-11-14 Thread ÏéÇ« ¿×

Dear Justin,
  Thanks for your prompt reply!
  As you say, we should equilibrium each replica at its initial target 
temperature. So i guess we may do the followings: First, after the minimization 
and heating, we use NPT to equilibrium the density of the system. And then with 
the same initial system,equilibrium every replica at their target temperature 
with NVT ensemble to avoid the instability during REMD and keep the volume 
constant among the replicas. Finally, do the REMD simulations. Is this workflow 
reasonable enough and do you have any better guide? Any suggestions will be 
greatly appreciated!
  
  Best regards!
  Xiangqian Kong








--- On Mon, 11/14/11, Justin A. Lemkul  wrote:

> From: Justin A. Lemkul 
> Subject: Re: [gmx-users] The equilibrium before REMD simulations
> To: "Discussion list for GROMACS users" 
> Date: Monday, November 14, 2011, 10:25 PM
> 
> 
> ÏéÇ« ¿× wrote:
> > Dear GMX users, I am puzzled about some technical
> details regarding to the
> > REMD simulation and eager for your generous help. With
> the purpose to explore
> > the additional conformational space of the protein, I
> want to employ the REMD
> > method in Gromacs. However, I noticed that in almost
> all of the papers about
> > REMD, a short equilibrium with NPT or NVT was
> performed for each replica
> > respectively before the final REMD run. But i think
> the initial structure of
> > each replica for REMD run is thus different due to the
> respective equilibrium
> > and may somewhat go against the concept of replicas
> which i suppose should
> > have same initial structures while with different
> temperatures. So my
> > question is whether we should or not perform the NVT
> or NPT equilibrium
> > before REMD simulations BTW and why? BTW, i also want
> to know which ensemble
> 
> Yes, always equilibrate.  Otherwise, your systems will
> almost certainly not be stable.  Position restraints
> are typically applied to the solute of interest during the
> initial equilibration, making initial differences almost
> insignificant.
> 
> > should we use in REMD because some papers use NPT
> while others use NVT. 
> 
> Pressure coupling algorithms frequently break down at high
> temperature, so NVT is often used.
> 
> -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] The equilibrium before REMD simulations

2011-11-14 Thread Justin A. Lemkul




ÏéÇ« ¿× wrote:

Dear Justin, Thanks for your prompt reply! As you say, we should equilibrium
each replica at its initial target temperature. So i guess we may do the
followings: First, after the minimization and heating, we use NPT to
equilibrium the density of the system. And then with the same initial
system,equilibrium every replica at their target temperature with NVT
ensemble to avoid the instability during REMD and keep the volume constant
among the replicas. Finally, do the REMD simulations. Is this workflow
reasonable enough and do you have any better guide? Any suggestions will be
greatly appreciated!



Seems reasonable, but I am no REMD expert.  There is certainly ample literature 
for you to read to find a suitable established protocol, or to validate your 
procedure.


-Justin


Best regards! Xiangqian Kong








--- On Mon, 11/14/11, Justin A. Lemkul  wrote:


From: Justin A. Lemkul  Subject: Re: [gmx-users] The
equilibrium before REMD simulations To: "Discussion list for GROMACS users"
 Date: Monday, November 14, 2011, 10:25 PM


ÏéÇ« ¿× wrote:

Dear GMX users, I am puzzled about some technical

details regarding to the

REMD simulation and eager for your generous help. With

the purpose to explore

the additional conformational space of the protein, I

want to employ the REMD

method in Gromacs. However, I noticed that in almost

all of the papers about

REMD, a short equilibrium with NPT or NVT was

performed for each replica

respectively before the final REMD run. But i think

the initial structure of

each replica for REMD run is thus different due to the

respective equilibrium

and may somewhat go against the concept of replicas

which i suppose should

have same initial structures while with different

temperatures. So my

question is whether we should or not perform the NVT

or NPT equilibrium

before REMD simulations BTW and why? BTW, i also want

to know which ensemble

Yes, always equilibrate.  Otherwise, your systems will almost certainly not
be stable.  Position restraints are typically applied to the solute of
interest during the initial equilibration, making initial differences
almost insignificant.


should we use in REMD because some papers use NPT

while others use NVT.

Pressure coupling algorithms frequently break down at high temperature, so
NVT is often used.

-Justin

-- 

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 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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MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
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http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Units of Buckingham potential

2011-11-14 Thread xiaojing gong

Many thanks for reply.
Another question, If I use Buckingham potential for CNT, and I want to
simulate CNT and water, shall I also transfer the SPC.itp from LJ to
Buckingham potential?
Best
XJ

2011/11/14 Mark Abraham 

> On 15/11/2011 2:00 AM, xiaojing gong wrote:
>
>> Hi dear all,
>> For Buckingham potential， there is three parameters A B C
>> In GMX, the units of A B C is the kJ/mol, nm, kJ/mol*nm^6， am I right?
>>
>
> Manual section 2.2 defines the units, and 4.1.2 defines the functional
> form.
>
> Mark
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Re: [gmx-users] The equilibrium before REMD simulations

2011-11-14 Thread Mark Abraham


On 15/11/2011 2:50 AM, ÏéÇ« ¿× wrote:

Dear Justin,
   Thanks for your prompt reply!
   As you say, we should equilibrium each replica at its initial target 
temperature. So i guess we may do the followings: First, after the minimization 
and heating, we use NPT to equilibrium the density of the system. And then with 
the same initial system,equilibrium every replica at their target temperature 
with NVT ensemble to avoid the instability during REMD and keep the volume 
constant among the replicas. Finally, do the REMD simulations. Is this workflow 
reasonable enough and do you have any better guide? Any suggestions will be 
greatly appreciated!



That is a standard REMD workflow. Do check out some literature for REMD 
simulations similar to your system.


Mark
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Re: [gmx-users] No locks available.

2011-11-14 Thread Roland Schulz

Hi,

On Mon, Nov 14, 2011 at 2:15 AM, lina  wrote:

> On Mon, Nov 14, 2011 at 7:47 AM, Roland Schulz  wrote:
> > Hi,
> > what file system is this? What operating system on the compute node? In
> case
> > it is a network file system what file system is used underneath and what
> > operating system is the file server using? What version of GROMACS are
> you
> > using?
> > As you workaround you should be able to run with "mdrun -noappend".
>
> There is no problem running a mdrun without appending.


Could you please send the information about your system? I would be
interested to see why it doesn't succeed to lock.

Roland



>  > Roland
> >
> > On Sun, Nov 13, 2011 at 10:43 AM, lina  wrote:
> >>
> >> Hi,
> >>
> >> This is the first time I met:
> >>
> >> Fatal error:
> >> Failed to lock: md.log. No locks available
> >>
> >> the disk is not saturated,
> >>
> >> md.log is normal,
> >>
> >> The job was stopped months ago, and now I planned to resume it with
> >> all the necessary files kept intact.
> >>
> >> Thanks for pointing out which parts I should examine,
> >>
> >> Best regards,
> >> --
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> >>
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> >
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[gmx-users] the force constant in constant speed umbrella pulling

2011-11-14 Thread Yun Shi

Hi everyone,

I am just wondering about the mathematical and physical meaning of this
force constant when pulling a ligand from its receptor.

So I can imagine a dummy atom is linked to the ligand via a spring, and it
is moving away from the receptor at 1 nm/ns with the spring force constant
1000 kJ/mol/nm^2. After it moved a very small distance, for example 0.0001
nm, which would be the change in the length of the spring, there will be a
corresponding force 0.1 kJ/mol/nm, which is 0.166 pN. So is this force only
directly exerted on the COM of the ligand? Or it's been distributed across
every atom within the ligand?

>From this imagined model, is seems the force constant does not have as much
effect on the quality (i.e. better quality means closer to a reversible
thermodynamic process) of the pulling process as the pulling rate. But I
wonder, would reducing force constant by 50% have the same effect on
decreasing computational load as reducing pulling rate by 50%? Supposing a
set pulled distance 5 nm is required, which one should save more
computational time?

Thanks for any suggestion.
Yun
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[gmx-users] UNK not found in residue topology

2011-11-14 Thread Janowicz, Adrianna C.







Hello,

I'm getting an UNK not found in residue topology error message.
After I run
pdb2gmx -f XXX.pdb -o conf.pdb

Fatal error:
Residue 'UNK' not found in residue topology database


I figured out what the error was and tried to add UNK as carbon to
ffopslaa.rtf

[UNK]
 [ atoms ]
UNK UNK  0.000 0

but I am still getting the same error. What do I do?

Adrianna





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[gmx-users] GMX to remove clashes?

2011-11-14 Thread Liu, Liang

Hi, all,
I am wondering if Gromacs can do the following work?

Assuming I have a pdb file of an RNA molecule. Some atoms may be too close
or even overlap, I am wondering if Gromacs can move the atoms to reasonable
positions and remove the bad contacts? The final structure is supposed to
be the "most" stable structure with minimal energy. I know AMBER
minimization can do this work, and I am wondering if Gromacs can do the
same?

-- 
Best,
Liang Liu
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Re: [gmx-users] GMX to remove clashes?

2011-11-14 Thread Justin A. Lemkul




Liu, Liang wrote:

Hi, all,
I am wondering if Gromacs can do the following work?

Assuming I have a pdb file of an RNA molecule. Some atoms may be too 
close or even overlap, I am wondering if Gromacs can move the atoms to 
reasonable positions and remove the bad contacts? The final structure is 
supposed to be the "most" stable structure with minimal energy. I know 
AMBER minimization can do this work, and I am wondering if Gromacs can 
do the same?




Gromacs is perfectly capable of energy minimization.  Whether or not 
minimization succeeds and gives a reasonable output is mostly dependent upon the 
feasibility of the starting structure.  If the minimization crashes, it's not 
Gromacs' fault ;)


-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] UNK not found in residue topology

2011-11-14 Thread Justin A. Lemkul




Janowicz, Adrianna C. wrote:






Hello,

I'm getting an UNK not found in residue topology error message.
After I run
pdb2gmx -f XXX.pdb -o conf.pdb

Fatal error:
Residue 'UNK' not found in residue topology database


I figured out what the error was and tried to add UNK as carbon to
ffopslaa.rtf



There are no .rtf files used by Gromacs, so if you've created or edited one, it 
will have no effect.



[UNK]
 [ atoms ]
UNK UNK  0.000 0

but I am still getting the same error. What do I do?



In theory, one can define a residue named UNK with atom names and types of UNK, 
but that's an incredibly awkward mechanism.  It would probably be worthwhile to 
use real, existing atom types (which would be required by OPLS) with a 
meaningful residue name.  Perhaps the format of your .pdb file is wrong and 
pdb2gmx is reading another column for the residue name instead of the one 
intended.  If you specify everything as UNK, you'll never know.


-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] GMX to remove clashes?

2011-11-14 Thread Liu, Liang

This is a "reasonable" answer :)

Thanks for that, and I just tried Gromacs for minimization, and looks the
final structure does not have clashes anymore, and also are very close to
the initial structure.

Another question is if there is a way to add ions automatically, meaning no
need to check the "NOTE" of "System has non-zero total charge" in the
output of grompp command? And also update the topology file automatically
too?

On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul  wrote:

>
>
> Liu, Liang wrote:
>
>> Hi, all,
>> I am wondering if Gromacs can do the following work?
>>
>> Assuming I have a pdb file of an RNA molecule. Some atoms may be too
>> close or even overlap, I am wondering if Gromacs can move the atoms to
>> reasonable positions and remove the bad contacts? The final structure is
>> supposed to be the "most" stable structure with minimal energy. I know
>> AMBER minimization can do this work, and I am wondering if Gromacs can do
>> the same?
>>
>>
> Gromacs is perfectly capable of energy minimization.  Whether or not
> minimization succeeds and gives a reasonable output is mostly dependent
> upon the feasibility of the starting structure.  If the minimization
> crashes, it's not Gromacs' fault ;)
>
> -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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> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
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>



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Liang Liu
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Re: [gmx-users] GMX to remove clashes?

2011-11-14 Thread Justin A. Lemkul




Liu, Liang wrote:

This is a "reasonable" answer :)

Thanks for that, and I just tried Gromacs for minimization, and looks 
the final structure does not have clashes anymore, and also are very 
close to the initial structure.


Another question is if there is a way to add ions automatically, meaning 
no need to check the "NOTE" of "System has non-zero total charge" in the 
output of grompp command? And also update the topology file 
automatically too?




That depends on the system.  For a simple solute in water, the running total 
charge of the solute is recorded in the qtot column of the .top file.  If you 
have a complex system with lots of charged things, no, there is no convenient 
way to get the charge aside from calculating it by hand or reading the grompp 
output.


The topology can be modified automatically by genion after ions are added by 
using the -p flag.


-Justin

On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul > wrote:




Liu, Liang wrote:

Hi, all,
I am wondering if Gromacs can do the following work?

Assuming I have a pdb file of an RNA molecule. Some atoms may be
too close or even overlap, I am wondering if Gromacs can move
the atoms to reasonable positions and remove the bad contacts?
The final structure is supposed to be the "most" stable
structure with minimal energy. I know AMBER minimization can do
this work, and I am wondering if Gromacs can do the same?


Gromacs is perfectly capable of energy minimization.  Whether or not
minimization succeeds and gives a reasonable output is mostly
dependent upon the feasibility of the starting structure.  If the
minimization crashes, it's not Gromacs' fault ;)

-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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--
Best,
Liang Liu


--


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] GMX to remove clashes?

2011-11-14 Thread Liu, Liang

Thanks.

Do you know how to use a new force field, not amber or charm, but a force
field built by someone else, and it's already in Gromacs format (tons of
xvg file, right?)

On Mon, Nov 14, 2011 at 4:13 PM, Justin A. Lemkul  wrote:

>
>
> Liu, Liang wrote:
>
>> This is a "reasonable" answer :)
>>
>> Thanks for that, and I just tried Gromacs for minimization, and looks the
>> final structure does not have clashes anymore, and also are very close to
>> the initial structure.
>>
>> Another question is if there is a way to add ions automatically, meaning
>> no need to check the "NOTE" of "System has non-zero total charge" in the
>> output of grompp command? And also update the topology file automatically
>> too?
>>
>>
> That depends on the system.  For a simple solute in water, the running
> total charge of the solute is recorded in the qtot column of the .top file.
>  If you have a complex system with lots of charged things, no, there is no
> convenient way to get the charge aside from calculating it by hand or
> reading the grompp output.
>
> The topology can be modified automatically by genion after ions are added
> by using the -p flag.
>
> -Justin
>
>  On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote:
>>
>>
>>
>>Liu, Liang wrote:
>>
>>Hi, all,
>>I am wondering if Gromacs can do the following work?
>>
>>Assuming I have a pdb file of an RNA molecule. Some atoms may be
>>too close or even overlap, I am wondering if Gromacs can move
>>the atoms to reasonable positions and remove the bad contacts?
>>The final structure is supposed to be the "most" stable
>>structure with minimal energy. I know AMBER minimization can do
>>this work, and I am wondering if Gromacs can do the same?
>>
>>
>>Gromacs is perfectly capable of energy minimization.  Whether or not
>>minimization succeeds and gives a reasonable output is mostly
>>dependent upon the feasibility of the starting structure.  If the
>>minimization crashes, it's not Gromacs' fault ;)
>>
>>-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
>>
>> 
>> >
>>
>>==**__==
>>
>>-- 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
>>
>>
>> 
>> >
>>
>>
>>
>>
>> --
>> Best,
>> Liang Liu
>>
>
> --
> ==**==
>
> 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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Liang Liu
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Plea

Re: [gmx-users] GMX to remove clashes?

2011-11-14 Thread Justin A. Lemkul

Liu, Liang wrote:

Thanks.

Do you know how to use a new force field, not amber or charm, but a 
force field built by someone else, and it's already in Gromacs format 
(tons of xvg file, right?)

Force fields are not in .xvg format, unless you're talking about using tabulated 
potentials.  In either case, please see the manual and the help information on 
gromacs.org, and start a new thread with more information to change topics if 
you have further questions.

-Justin

On Mon, Nov 14, 2011 at 4:13 PM, Justin A. Lemkul > wrote:

Liu, Liang wrote:

This is a "reasonable" answer :)

Thanks for that, and I just tried Gromacs for minimization, and
looks the final structure does not have clashes anymore, and
also are very close to the initial structure.

Another question is if there is a way to add ions automatically,
meaning no need to check the "NOTE" of "System has non-zero
total charge" in the output of grompp command? And also update
the topology file automatically too?

That depends on the system.  For a simple solute in water, the
running total charge of the solute is recorded in the qtot column of
the .top file.  If you have a complex system with lots of charged
things, no, there is no convenient way to get the charge aside from
calculating it by hand or reading the grompp output.

The topology can be modified automatically by genion after ions are
added by using the -p flag.

-Justin

On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul
mailto:jalem...@vt.edu>
>> wrote:

   Liu, Liang wrote:

   Hi, all,
   I am wondering if Gromacs can do the following work?

   Assuming I have a pdb file of an RNA molecule. Some atoms
may be
   too close or even overlap, I am wondering if Gromacs can move
   the atoms to reasonable positions and remove the bad
contacts?
   The final structure is supposed to be the "most" stable
   structure with minimal energy. I know AMBER minimization
can do
   this work, and I am wondering if Gromacs can do the same?

   Gromacs is perfectly capable of energy minimization.  Whether
or not
   minimization succeeds and gives a reasonable output is mostly
   dependent upon the feasibility of the starting structure.  If the
   minimization crashes, it's not Gromacs' fault ;)

   -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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-- 
Best,

Liang Liu

-- 
==__==

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.e

[gmx-users] import force field

2011-11-14 Thread Liu, Liang

I have a serial of tabulated potentials with the name of *.xvg, which are
the function of atom distance.
I am wondering how to use them in gromacs simulation? Will that replace the
force field, e.g. amber03? Thanks.

-- 
Best,
Liang Liu
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RE: [gmx-users] Time unit issue with g_anaeig

2011-11-14 Thread Kei Sit

Hi Mark,

I ran gmxcheck and it returned the following output:

Checking file 1-21.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  7764
Reading frame   49000 time 4900.000


Item#frames Timestep (ps)
Step 499840.1
Time 499840.1
Lambda   499840.1
Coords   499840.1
Velocities   0
Forces   0
Box  499840.1

I understand now why the time is 10 times smaller in my analysis, but this now 
raises another question as to why it is 0.1ps per frame. Would it have 
something to do with the converting from a DCD format to a TRR format? I just 
checked the configuration file for my MD run and I can still see that I'm 
running the simulation of 2fs timesteps and saving output every 500 steps which 
should equate to 1ps. Once again, thank you for your time in helping.

Regards,
Kei

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Mark Abraham
Sent: Monday, 14 November 2011 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Time unit issue with g_anaeig

On 14/11/2011 5:46 PM, Kei Sit wrote:
Hi all,

I'm new to gromacs so I hope I haven't done something wrong that is extremely 
simple. I have recently been using gromacs to analyse an MD trajectory using 
g_covar and g_anaeig. I have output saved to the trajectory every ps and I 
currently have a trajectory with 49000 frames (49ns).

I initiate g_anaeig with this command:

g_anaeig -v eigenvec.trr  -f 1-21.trr -s protein.pdb -eig eigenval.xvg -proj 
projection.xvg -xvgr -first 1 -last 8

While this is being executed I see this:

Reading frame 1000 time 100.00

which continues increasing as more frames are read.

When I go to visualise projection.xvg, the time scale is in ps (natural as the 
default value is in ps) but it only shows 4900ps and not 49000ps.

My issue is  this, why is the time constantly 10 times smaller than the number 
of frames that are being read? Am I not entering something correctly which 
fixes this?


What does gmxcheck have to say about your trajectory files?

Mark
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[gmx-users] Query on restraining center of mass of a protein

2011-11-14 Thread Sanku M

Hi,
  I have a system containing water and a large protein. In the simulation, I do 
not want the protein center of mass to drift away. I was wondering what will be 
the reasonable method in gromacs to fix the position of the center of mass of 
the protein in its original position . I was thinking about two options in 
gromacs.
  1) use the protein as comm-grp only to remove its center of mass motion . ( 
or should I use both protein and non-protein ( water) center of mass as 
comm-grps separately ).
  2) Finding the residue closest to center of mass of the protein ( but I am 
not sure how to do it ).
Can anyone suggest which will be a good idea ?

Sanku-- 
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RE: [gmx-users] Time unit issue with g_anaeig

2011-11-14 Thread Kei Sit

Hi again,

I just found the solution to the problem. Using trjconv to specify the timestep 
seems to have helped. Thanks again for the help.

Regards,
Kei

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Kei Sit
Sent: Tuesday, 15 November 2011 9:20 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] Time unit issue with g_anaeig

Hi Mark,

I ran gmxcheck and it returned the following output:

Checking file 1-21.trr
trn version: GMX_trn_file (single precision)
Reading frame   0 time0.000
# Atoms  7764
Reading frame   49000 time 4900.000


Item#frames Timestep (ps)
Step 499840.1
Time 499840.1
Lambda   499840.1
Coords   499840.1
Velocities   0
Forces   0
Box  499840.1

I understand now why the time is 10 times smaller in my analysis, but this now 
raises another question as to why it is 0.1ps per frame. Would it have 
something to do with the converting from a DCD format to a TRR format? I just 
checked the configuration file for my MD run and I can still see that I'm 
running the simulation of 2fs timesteps and saving output every 500 steps which 
should equate to 1ps. Once again, thank you for your time in helping.

Regards,
Kei

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Mark Abraham
Sent: Monday, 14 November 2011 6:47 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Time unit issue with g_anaeig

On 14/11/2011 5:46 PM, Kei Sit wrote:
Hi all,

I'm new to gromacs so I hope I haven't done something wrong that is extremely 
simple. I have recently been using gromacs to analyse an MD trajectory using 
g_covar and g_anaeig. I have output saved to the trajectory every ps and I 
currently have a trajectory with 49000 frames (49ns).

I initiate g_anaeig with this command:

g_anaeig -v eigenvec.trr  -f 1-21.trr -s protein.pdb -eig eigenval.xvg -proj 
projection.xvg -xvgr -first 1 -last 8

While this is being executed I see this:

Reading frame 1000 time 100.00

which continues increasing as more frames are read.

When I go to visualise projection.xvg, the time scale is in ps (natural as the 
default value is in ps) but it only shows 4900ps and not 49000ps.

My issue is  this, why is the time constantly 10 times smaller than the number 
of frames that are being read? Am I not entering something correctly which 
fixes this?


What does gmxcheck have to say about your trajectory files?

Mark
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Re: [gmx-users] Query on restraining center of mass of a protein

2011-11-14 Thread Mark Abraham


On 15/11/2011 10:21 AM, Sanku M wrote:

Hi,
  I have a system containing water and a large protein. In the 
simulation, I do not want the protein center of mass to drift away.


Why do you want it not to drift away? There's nothing magical about the 
center of a periodic simulation cell. Why do you want to change the 
dynamics to achieve this?


Mark

I was wondering what will be the reasonable method in gromacs to fix 
the position of the center of mass of the protein in its original 
position . I was thinking about two options in gromacs.
  1) use the protein as comm-grp only to remove its center of mass 
motion . ( or should I use both protein and non-protein ( water) 
center of mass as comm-grps separately ).
  2) Finding the residue closest to center of mass of the protein ( 
but I am not sure how to do it ).

Can anyone suggest which will be a good idea ?




-- 
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Re: [gmx-users] import force field

2011-11-14 Thread Mark Abraham


On 15/11/2011 9:33 AM, Liu, Liang wrote:
I have a serial of tabulated potentials with the name of *.xvg, which 
are the function of atom distance.
I am wondering how to use them in gromacs simulation? Will that 
replace the force field, e.g. amber03? Thanks.


There are sections in the manual that describe the use of tabulated 
potentials for either bonded or non-bonded interactions. Such tables 
modify the force field in the expected manner.


Mark
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[gmx-users] Questionable van der waals volumes from g_sas

2011-11-14 Thread Jacob Alan Spooner

Hello gmx-users

I have been attempting to obtain van der Waal's volumes using the g_sas 
utility.  The command I use to do so is something like

g_sas -f hexane.gro -s topol.tpr -probe 0 -tv V_vdw.xvg

This seems to give reasonable results for most of my test systems, however when 
I run the command on an optimized structure of cyclohexane I get a larger van 
der Waal's volume than that of n-hexane.  I think this has to do with the fact 
that the surface calculation method used in g_sas is missing the void in the 
centre of the ring.  In order to test this I increased the size of the ring, 
calculating the volumes of icosane and cycloicosane.  I found that in this case 
the volume of the cyclic molecule was expectedly smaller.  I tried increasing 
the number of dots used to draw the dot-surface but saw no significant change 
in the volumes.

Therefore my question is if anybody is familiar enough with g_sas to help me 
understand why the surface calculation method is not giving sensible values for 
these smaller ring systems.  Also I am wondering if anybody can suggest any 
other free software that would allow me to compute van der Waal's and Solvent 
Excluded volumes.

Thanks in advance.

Jake Spooner
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Re: [gmx-users] The equilibrium before REMD simulations

2011-11-14 Thread ÏéÇ« ¿×

Thanks for everyone's prompt reply! However, i still puzzled why we should use 
NVT rather than NPT in REMD simulation. As we know that isothermal-isobaric 
ensemble may be more relevant to the realistic experimental conditions. If the 
highest temperature was no more than 400K ( i think it is not very high) and 
the pressure coupling may still work, should NPT be a better choice? Or the NPT 
method would impair the physical meanings of REMD, however, some NPT examples 
were depicted in some papers and also in our mailing list.

Best regards!
Xiangqian Kong

--- On Mon, 11/14/11, Mark Abraham  wrote:

> From: Mark Abraham 
> Subject: Re: [gmx-users] The equilibrium before REMD simulations
> To: "Discussion list for GROMACS users" 
> Date: Monday, November 14, 2011, 11:53 PM
> On 15/11/2011 2:50 AM, ÏéÇ« ¿×
> wrote:
> > Dear Justin,
> >    Thanks for your prompt reply!
> >    As you say, we should equilibrium each
> replica at its initial target temperature. So i guess we may
> do the followings: First, after the minimization and
> heating, we use NPT to equilibrium the density of the
> system. And then with the same initial system,equilibrium
> every replica at their target temperature with NVT ensemble
> to avoid the instability during REMD and keep the volume
> constant among the replicas. Finally, do the REMD
> simulations. Is this workflow reasonable enough and do you
> have any better guide? Any suggestions will be greatly
> appreciated!
> > 
> 
> That is a standard REMD workflow. Do check out some
> literature for REMD simulations similar to your system.
> 
> Mark
> -- gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] The equilibrium before REMD simulations

2011-11-14 Thread Mark Abraham


On 15/11/2011 11:55 AM, ÏéÇ« ¿× wrote:

Thanks for everyone's prompt reply! However, i still puzzled why we should use 
NVT rather than NPT in REMD simulation. As we know that isothermal-isobaric 
ensemble may be more relevant to the realistic experimental conditions. If the 
highest temperature was no more than 400K ( i think it is not very high) and 
the pressure coupling may still work, should NPT be a better choice? Or the NPT 
method would impair the physical meanings of REMD, however, some NPT examples 
were depicted in some papers and also in our mailing list.


Yes, NPT REMD appears to be quite sound. However, unless you actually 
want to make measurements of physical observables at the higher 
temperatures, there's no requirement that the higher ensembles 
correspond to any particular physical model - see things like resolution 
replica-exchange. A coordinate mapping, a sufficiency of PE overlap and 
the possibility of barrier crossing are all that is required for useful 
replica exchange.


There are also some technical issues associated with density in NPT. 
Because the lists of non-bonded interactions are shorter when the 
density is lower, the higher-temperature replicas have less work to do, 
so have to waste some computer time waiting for the lower ones to 
finish. That's not a big deal, but if you want to use PME and maintain 
accuracy, the Fourier grid density should change inversely with particle 
density, and that gets a bit messy.


Issues with the size of the integration time step at high P and T have 
also been known to occur.


Mark



Best regards!
Xiangqian Kong

--- On Mon, 11/14/11, Mark Abraham  wrote:


From: Mark Abraham
Subject: Re: [gmx-users] The equilibrium before REMD simulations
To: "Discussion list for GROMACS users"
Date: Monday, November 14, 2011, 11:53 PM
On 15/11/2011 2:50 AM, ÏéÇ« ¿×
wrote:

Dear Justin,
 Thanks for your prompt reply!
 As you say, we should equilibrium each

replica at its initial target temperature. So i guess we may
do the followings: First, after the minimization and
heating, we use NPT to equilibrium the density of the
system. And then with the same initial system,equilibrium
every replica at their target temperature with NVT ensemble
to avoid the instability during REMD and keep the volume
constant among the replicas. Finally, do the REMD
simulations. Is this workflow reasonable enough and do you
have any better guide? Any suggestions will be greatly
appreciated!
That is a standard REMD workflow. Do check out some
literature for REMD simulations similar to your system.

Mark
-- gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] RE: Questionable van der waals volumes from g_sas

2011-11-14 Thread Dallas Warren

Sorry, ignore my last post, only just realised you had set your probe to 0 
radius.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Jacob Alan Spooner
Sent: Tuesday, 15 November 2011 11:29 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Questionable van der waals volumes from g_sas

Hello gmx-users

I have been attempting to obtain van der Waal's volumes using the g_sas 
utility.  The command I use to do so is something like

g_sas -f hexane.gro -s topol.tpr -probe 0 -tv V_vdw.xvg

This seems to give reasonable results for most of my test systems, however when 
I run the command on an optimized structure of cyclohexane I get a larger van 
der Waal's volume than that of n-hexane.  I think this has to do with the fact 
that the surface calculation method used in g_sas is missing the void in the 
centre of the ring.  In order to test this I increased the size of the ring, 
calculating the volumes of icosane and cycloicosane.  I found that in this case 
the volume of the cyclic molecule was expectedly smaller.  I tried increasing 
the number of dots used to draw the dot-surface but saw no significant change 
in the volumes.

Therefore my question is if anybody is familiar enough with g_sas to help me 
understand why the surface calculation method is not giving sensible values for 
these smaller ring systems.  Also I am wondering if anybody can suggest any 
other free software that would allow me to compute van der Waal's and Solvent 
Excluded volumes.

Thanks in advance.

Jake Spooner
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] RE: Questionable van der waals volumes from g_sas

2011-11-14 Thread Dallas Warren

Jake,

Wont the volume be a function of the probe radius that is used?  And hence, if 
it is too big to fit through the ring, the volume will be larger than if the 
chain was straight?

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On 
Behalf Of Jacob Alan Spooner
Sent: Tuesday, 15 November 2011 11:29 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Questionable van der waals volumes from g_sas

Hello gmx-users

I have been attempting to obtain van der Waal's volumes using the g_sas 
utility.  The command I use to do so is something like

g_sas -f hexane.gro -s topol.tpr -probe 0 -tv V_vdw.xvg

This seems to give reasonable results for most of my test systems, however when 
I run the command on an optimized structure of cyclohexane I get a larger van 
der Waal's volume than that of n-hexane.  I think this has to do with the fact 
that the surface calculation method used in g_sas is missing the void in the 
centre of the ring.  In order to test this I increased the size of the ring, 
calculating the volumes of icosane and cycloicosane.  I found that in this case 
the volume of the cyclic molecule was expectedly smaller.  I tried increasing 
the number of dots used to draw the dot-surface but saw no significant change 
in the volumes.

Therefore my question is if anybody is familiar enough with g_sas to help me 
understand why the surface calculation method is not giving sensible values for 
these smaller ring systems.  Also I am wondering if anybody can suggest any 
other free software that would allow me to compute van der Waal's and Solvent 
Excluded volumes.

Thanks in advance.

Jake Spooner
-- 
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http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] No locks available.

2011-11-14 Thread lina

On Mon, Nov 14, 2011 at 7:47 AM, Roland Schulz  wrote:
> Hi,

Well, thanks, here comes the questions you asked before.

> what file system is this? What operating system on the compute node? In case
> it is a network file system what file system is used underneath and what
> operating system is the file server using? What version of GROMACS are you
> using?

CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz
Memory: 114GB RAM
HDD Size: 744GB
OS: CentOS 4 (64-bits)

2.6.9-42.0.10.ELlargesmp #1 SMP Tue Feb 27 09:59:08 EST 2007 x86_64
x86_64 x86_64 GNU/Linux

Gromacs, VERSION 4.5.3

If you need more information, please feel free to let me know.

Best regards,

> As you workaround you should be able to run with "mdrun -noappend".
> Roland
>
> On Sun, Nov 13, 2011 at 10:43 AM, lina  wrote:
>>
>> Hi,
>>
>> This is the first time I met:
>>
>> Fatal error:
>> Failed to lock: md.log. No locks available
>>
>> the disk is not saturated,
>>
>> md.log is normal,
>>
>> The job was stopped months ago, and now I planned to resume it with
>> all the necessary files kept intact.
>>
>> Thanks for pointing out which parts I should examine,
>>
>> Best regards,
>> --
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>>
>>
>>
>>
>
>
>
> --
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> 865-241-1537, ORNL PO BOX 2008 MS6309
>
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[gmx-users] how to select option for genion command automatically?

2011-11-14 Thread Liu, Liang

I am wondering if there is a flag to make the command select SOL
automatically instead of pressing some number each time? I have thousands
of structures, it is really time-consuming to select one by one.

-- 
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Liang Liu
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Re: [gmx-users] how to select option for genion command automatically?

2011-11-14 Thread Justin A. Lemkul




Liu, Liang wrote:
I am wondering if there is a flag to make the command select SOL 
automatically instead of pressing some number each time? I have 
thousands of structures, it is really time-consuming to select one by one.




Yes, there is:

http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

-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] how to select option for genion command automatically?

2011-11-14 Thread Terry

This is what you are looking for:

http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts?highlight=scripting

Terry


On Tue, Nov 15, 2011 at 11:42 AM, Liu, Liang  wrote:

> I am wondering if there is a flag to make the command select SOL
> automatically instead of pressing some number each time? I have thousands
> of structures, it is really time-consuming to select one by one.
>
> --
> Best,
> Liang Liu
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] how to select option for genion command automatically?

2011-11-14 Thread Liu, Liang

Yes, I found it. THanks.

On Mon, Nov 14, 2011 at 9:45 PM, Terry  wrote:

>
> This is what you are looking for:
>
>
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts?highlight=scripting
>
> Terry
>
>
> On Tue, Nov 15, 2011 at 11:42 AM, Liu, Liang  wrote:
>
>> I am wondering if there is a flag to make the command select SOL
>> automatically instead of pressing some number each time? I have thousands
>> of structures, it is really time-consuming to select one by one.
>>
>> --
>> Best,
>> Liang Liu
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>
>
>
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Re: [gmx-users] Positive potential energy for TFE solvent

2011-11-14 Thread Harpreet Basra

Hi


I am still stuck with same problem of obtaining positive potential energy.

>>On 11/11/2011 5:07 PM, Harpreet Basra wrote:
>> Hi
>>
>> I am trying to generate an equilibrated box of 216 TFE molecules.To
>> generate the 216 TFE molecule box i performed following steps:
>
>A suggested workflow can be found here
>http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation

I have been following this link only.

>
>
>> 1) I got the tfe.gro file and created a cubic box of edge length =
>> 0.516 nm containing 1 TFE molecule (at its center), using the
>> following command:
>>
 editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516
>>  I chose this length because in the tfe.gro file dimensions of the TFE
>> molecule are 0.516 0.516 0.516.
>
>That's not a good reason. Choose a volume and shape that makes sense for
>your target density. Cubic probably doesn't make sense when a
>rectangular shape is possible. Then you'll probably want to choose -nbox
>differently later.

I chose a rectangular box too. still i get a positive value for PE and
moreover all the molecules move towards two opposite walls of the box. I am
not sure that the way I am using the genconf command is the correct way.
because I have tried every other possibility for not getting a positive
potential, with no success. So here are my .gro file and the topology file
for TFE.

*tfe.gro file*

 7

1TFE   F1T   1   0.444   0.344   0.246

1TFE   CT 2   0.334  0.245   0.246

1TFE   F2T3   0.350  0.160   0.364

1TFE   F3T4   0.350  0.160   0.127

1TFE   CH2T  5  0.187  0.326   0.246

1TFE   OT  6  0.075  0.220   0.246

1TFE   HT  7  -0.019 0.266   0.246

0.49174   0.49174   0.49174



topology file

[ moleculetype ]

; Name nrexcl

TFE 3

[ atoms ]

; nr type resnr resid atom cgnr charge mass

1 FTFE1  TFE  F1T   1   -0.170   18.9984

2 CTFE1  TFE  CT10.452   12.0110

3 FTFE1  TFE  F2T   1   -0.170   18.9984

4 FTFE1  TFE  F3T   1   -0.170   18.9984

5 CHTFE 1  TFE  CH2T 10.273   14.0270

6 OTFE   1  TFE  OT 1   -0.625   15.9994

7 H  1  TFE  HT 1   0.410   1.0080

[ bonds ]

; ai aj fu c0, c1, ...

2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1

2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2

2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3

2 5 2 0.153 715.0 0.153 715.0 ; C1 C2

5 6 2 0.143 818.0 0.143 818.0 ; C2 O

6 7 2 0.100 1570.0 0.100 1570.0 ; O H

[ pairs ]

; ai aj fu c0, c1, ...

1 6 1 ; F1 O

2 7 1 ; C1 H

3 6 1 ; F2 O

4 6 1 ; F3 O

[ angles ]

; ai aj ak fu c0, c1, ...

1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2

1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3

1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2

3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3

3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2

4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2

2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O

5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H

[ dihedrals ]

; ai aj ak al fu c0, c1, m, ...

6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1

2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H

and to construct a box of TFE solvent i took the tfe.gro file and
replicated the TFE molecule by using


genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6


can u plz suggest is it that I am using genconf in a wrong way that it is
causing this problem? I am not sure how many molecules (-nbox option in
genconf) should i keep in the box in order to get a mass density of 1383g/L
for TFE.

thanks

Harpreet

>
>> 2) Then using genconf command i replicated the box to get a bigger box
>> with 216 TFE molecules using the following command:
>>
 genconf -f tfe_box.gro  -o out.gro -rot -nbox 6
>> 3) Energy minimization was done using STEEPEST descent
>>
>> 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns
>> NPT (300K, 1atm) equilibration.
>>
>> After doing all these steps still I obtain a positive a potentail
>> energy. I get positive potential energy of the system (2.45+E04
>> kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive
>> total energy of the system. My question is whether obtaining positive
>> potential energy indicate some error in my TFE solvent box ? Is it
>> because of large Fluorine atoms of TFE ? Does it mean its not properly
>> equilibrated ? What can I do to equilibrate it?
>
>You probably have atomic overlaps from your choice of cubic 0.516 box
>earlier. Did you look at the results of genconf before computing with them?
>
>Mark
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Re: [gmx-users] Positive potential energy for TFE solvent

2011-11-14 Thread Mark Abraham


On 15/11/2011 6:06 PM, Harpreet Basra wrote:

Hi
I am still stuck with same problem of obtaining positive potential 
energy.

>>On 11/11/2011 5:07 PM, Harpreet Basra wrote:
>> Hi
>>
>> I am trying to generate an equilibrated box of 216 TFE molecules.To
>> generate the 216 TFE molecule box i performed following steps:
>
>A suggested workflow can be found here
>http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
I have been following this link only.
>
>
>> 1) I got the tfe.gro file and created a cubic box of edge length =
>> 0.516 nm containing 1 TFE molecule (at its center), using the
>> following command:
>>
 editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516
>>  I chose this length because in the tfe.gro file dimensions of the TFE
>> molecule are 0.516 0.516 0.516.
>
>That's not a good reason. Choose a volume and shape that makes sense for
>your target density. Cubic probably doesn't make sense when a
>rectangular shape is possible. Then you'll probably want to choose -nbox
>differently later.
I chose a rectangular box too. still i get a positive value for PE and 
moreover all the molecules move towards two opposite walls of the box. 
I am not sure that the way I am using the genconf command is the 
correct way. because I have tried every other possibility for not 
getting a positive potential, with no success. So here are my .gro 
file and the topology file for TFE.

*tfe.gro file*
7

1TFE   F1T   1   0.444   0.344   0.246

1TFE   CT 2   0.334  0.245   0.246

1TFE   F2T3   0.350  0.160   0.364

1TFE   F3T4   0.350  0.160   0.127

1TFE   CH2T  5  0.187  0.326   0.246

1TFE   OT  6  0.075  0.220   0.246

1TFE   HT  7  -0.019 0.266   0.246

0.49174   0.49174   0.49174

topology file

[ moleculetype ]

; Name nrexcl

TFE 3

[ atoms ]

; nr type resnr resid atom cgnr charge mass

1 FTFE1  TFE  F1T   1   -0.170   18.9984

2 CTFE1  TFE  CT10.452   12.0110

3 FTFE1  TFE  F2T   1   -0.170   18.9984

4 FTFE1  TFE  F3T   1   -0.170   18.9984

5 CHTFE 1  TFE  CH2T 10.273   14.0270

6 OTFE   1  TFE  OT 1   -0.625   15.9994

7 H  1  TFE  HT 1   0.410   1.0080

[ bonds ]

; ai aj fu c0, c1, ...

2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1

2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2

2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3

2 5 2 0.153 715.0 0.153 715.0 ; C1 C2

5 6 2 0.143 818.0 0.143 818.0 ; C2 O

6 7 2 0.100 1570.0 0.100 1570.0 ; O H

[ pairs ]

; ai aj fu c0, c1, ...

1 6 1 ; F1 O

2 7 1 ; C1 H

3 6 1 ; F2 O

4 6 1 ; F3 O

[ angles ]

; ai aj ak fu c0, c1, ...

1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2

1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3

1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2

3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3

3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2

4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2

2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O

5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H

[ dihedrals ]

; ai aj ak al fu c0, c1, m, ...

6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1

2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H

and to construct a box of TFE solvent i took the tfe.gro file and 
replicated the TFE molecule by using

genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6
can u plz suggest is it that I am using genconf in a wrong way that it 
is causing this problem? I am not sure how many molecules (-nbox 
option in genconf) should i keep in the box in order to get a mass 
density of 1383g/L for TFE.


That link says "Work out how much volume a single molecule would have in 
the box of your chosen density and size. Useeditconf 
to place a box of that size around your 
single molecule." It does not seem to me that you have done this.


Mark


thanks
Harpreet
>
>> 2) Then using genconf command i replicated the box to get a bigger box
>> with 216 TFE molecules using the following command:
>>
 genconf -f tfe_box.gro  -o out.gro -rot -nbox 6
>> 3) Energy minimization was done using STEEPEST descent
>>
>> 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns
>> NPT (300K, 1atm) equilibration.
>>
>> After doing all these steps still I obtain a positive a potentail
>> energy. I get positive potential energy of the system (2.45+E04
>> kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive
>> total energy of the system. My question is whether obtaining positive
>> potential energy indicate some error in my TFE solvent box ? Is it
>> because of large Fluorine atoms of TFE ? Does it mean its not properly
>> equilibrated ? What can I do to equilibrate it?
>
>You probably have atomic overlaps from your choice of cubic 0.516 box
>earlier. Did you look at the results of genconf before computing with 
them?

>
>Mark




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[gmx-users] Re: Positive potential energy for TFE solvent

2011-11-14 Thread Harpreet Basra

hi,

I am still stuck with same problem of obtaining positive potential energy.

>>On 11/11/2011 5:07 PM, Harpreet Basra wrote:
>> Hi
>>
>> I am trying to generate an equilibrated box of 216 TFE molecules.To
>> generate the 216 TFE molecule box i performed following steps:
>
>A suggested workflow can be found here
>http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation

I have been following this link only.

>
>
>> 1) I got the tfe.gro file and created a cubic box of edge length =
>> 0.516 nm containing 1 TFE molecule (at its center), using the
>> following command:
>>
 editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516
>>  I chose this length because in the tfe.gro file dimensions of the TFE
>> molecule are 0.516 0.516 0.516.
>
>That's not a good reason. Choose a volume and shape that makes sense for
>your target density. Cubic probably doesn't make sense when a
>rectangular shape is possible. Then you'll probably want to choose -nbox
>differently later.

I chose a rectangular box too. still i get a positive value for PE and
moreover all the molecules move towards two opposite walls of the box. I am
not sure that the way I am using the genconf command is the correct way.
because I have tried every other possibility for not getting a positive
potential, with no success. So here are my .gro file and the topology file
for TFE.

 the energy of this one molecule (tfe.gro) was coming out to b e highly
negative (-6.4E+08 kJ/mol). But on generating a solvent system with 216
molecules the energy becomes (1.9E+04 kJ/mol).

**tfe.gro file*

 7
1TFE   F1T   1   0.444   0.344   0.246
1TFE   CT 2   0.334  0.245   0.246
1TFE   F2T3   0.350  0.160   0.364
1TFE   F3T4   0.350  0.160   0.127
1TFE   CH2T  5  0.187  0.326   0.246
1TFE   OT  6  0.075  0.220   0.246
1TFE   HT  7  -0.019 0.266   0.246
0.49174   0.49174   0.49174

topology file
[ moleculetype ]
; Name nrexcl
TFE 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 FTFE1  TFE  F1T   1   -0.170   18.9984
2 CTFE1  TFE  CT10.452   12.0110
3 FTFE1  TFE  F2T   1   -0.170   18.9984
4 FTFE1  TFE  F3T   1   -0.170   18.9984
5 CHTFE 1  TFE  CH2T 10.273   14.0270
6 OTFE   1  TFE  OT 1   -0.625   15.9994
7 H  1  TFE  HT 1   0.410   1.0080
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1
2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2
2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3
2 5 2 0.153 715.0 0.153 715.0 ; C1 C2
5 6 2 0.143 818.0 0.143 818.0 ; C2 O
6 7 2 0.100 1570.0 0.100 1570.0 ; O H
[ pairs ]
; ai aj fu c0, c1, ...
1 6 1 ; F1 O
2 7 1 ; C1 H
3 6 1 ; F2 O
4 6 1 ; F3 O
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2
1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3
1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2
3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3
3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2
4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2
2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O
5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1
2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H

To construct a box of TFE solvent i took the tfe.gro file and replicated
the TFE molecule by using


genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6


can u plz suggest is it that I am using genconf in a wrong way that it is
causing this problem? I am not sure how many molecules (-nbox option in
genconf) should i keep in the box in order to get a mass density of 1383g/L
for TFE. Though i checked the denity of solvent box i constructed the
average valu comes out to be 1397g/L with a std deviation of 30g/L. thus
it seems range.

thanks

Harpreet

>
>> 2) Then using genconf command i replicated the box to get a bigger box
>> with 216 TFE molecules using the following command:
>>
 genconf -f tfe_box.gro  -o out.gro -rot -nbox 6
>> 3) Energy minimization was done using STEEPEST descent
>>
>> 4) Then I performed 5ns NVT (300K) equilibration and followed by 5ns
>> NPT (300K, 1atm) equilibration.
>>
>> After doing all these steps still I obtain a positive a potentail
>> energy. I get positive potential energy of the system (2.45+E04
>> kJ/mol) and kinetic energy as 4.03+E03 kJ/mol, thus giving a positive
>> total energy of the system. My question is whether obtaining positive
>> potential energy indicate some error in my TFE solvent box ? Is it
>> because of large Fluorine atoms of TFE ? Does it mean its not properly
>> equilibrated ? What can I do to equilibrate it?
>
>You probably have atomic overlaps from your choice of cubic 0.516 box
>earlier. Did you look at the results of genconf before computing with them?
>
>Mark
-- 
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