Nilesh Dhumal wrote:
Hello Justin,
I am using Gromacs 4.0.5 version.
I am getting the same error without specifying -o option.
You could try upgrading to 4.0.7, but I don't know if there have been any
changes in the code that would affect this behavior. Otherwise, submit a bugzilla.
-Justin
Nilesh
On Thu, April 22, 2010 5:07 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello Justin
In manual (Manual-4.0) and g_nmens -h (help), the extension of output
file is .xtc. If I use the default output file name still I am getting
the same error.
I know what the help information says, I was just trying to clarify if
what you had shown was actually a direct copy-and-paste from a terminal or
something else processed through your memory. Whether or not you were
specifying the same output name as default (or thought you were) is
irrelevant, I was just suggesting a test - don't specify anything at all
for the -o flag, just in case you made some sort of typo. If you get the
same error when you are not specifying anything at all with -o, then at
least post the Gromacs version you're using (which I asked for before) to
see if any of the developers has an idea about what could be going on. If
the default output is giving a fatal error, something is probably wrong in
the code.
-Justin
Nilesh
On Thu, April 22, 2010 4:01 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello Justin,
I could genrate the .mtx file. I followed following steps.
g_nmeig -f test.mtx -s 1.tpr -of eigenfreq.xvg -v test1.trr
g_nmtraj -s 1.tpr -v test1.trr -o test.xtc
g_anaeig -v test1.trr -f test.xtc -s 1.tpr -eig eigenval.xvg
and
g_nmens -v test1.trr -e eigenval.xvg -n test.ndx -s 1.tpr -o
ensemble.xtc
For last analysis (g_nmens) I get following error.
Fatal error:Sorry, write_trxframe_indexed can not write tpa
Can you help me resolve this error.
Did the above g_nmens command come directly from a copy-paste from
your terminal? Looking into the code, I see no way that writing an
.xtc file
would be misinterpreted as writing a binary topology, thus giving that
error. Check for typos, specifically in the file extension. If
you're using the default output file name, you don't even have to
specify it.
If it still doesn't work, report back. It might also be useful to
know your Gromacs version in case of problems.
-Justin
NIlesh
On Thu, April 22, 2010 12:55 pm, Justin A. Lemkul wrote:
Nilesh Dhumal wrote:
Hello,
I am trying to calculate the normal mode analysis for ionic
liquids. I could do energy minimzation. I could not get .mtx
file for further analysis to get normal modes.
THis is my energy minimization file
define = -DFLEXIBLE
constraints = none
integrator = L-bfgs
tinit = 0
nsteps = 15000
nbfgscorr = 50
emtol = .001
emstep = 0.1
gen_vel = yes
gen-temp = 300
nstcomm = 1
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 0
; ns algorithm (simple or grid)
ns-type = simple
; Periodic boundary conditions: xyz (default), no (vacuum)
; or full (infinite systems only)
pbc = no
; nblist cut-off
rlist = 0
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Cut-Off
rcoulomb-switch = 0
rcoulomb = 0
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 0
grompp -f minim.mdp -t 1.trr -c test.pdb -o 1.tpr -zero -p
test.top
Be careful about setting -zero. If you're trying to get past
error messages, that usually means you have missing parameters and
could end up with nonsense as a result.
mdrun -v -s 1.tpr -deffnm new_nm -mtx new_nm.mtx
I could not get the new_nm.mtx file.
Can you tell me where I am going wrong.
You aren't getting the .mtx file because you're telling mdrun to
do energy minimization, not normal modes. L-BFGS is an EM method.
Set
"integrator = nm"
to do normal modes.
-Justin
THanks
Nilesh
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
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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Please search the archive at http://www.gromacs.org/search before posting!
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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