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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