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On 4/27/2011 11:52 AM, MD wrote:
<blockquote
cite="mid:1607364c.2c12.12f94a82c2d.Coremail.ptf1242@163.com"
type="cite">Hi Justin,<br>
<br>
When i define <br>
<br>
<pre>define = FLEXIBLE
</pre>
</blockquote>
<br>
This is not of the correct form.<br>
<br>
<blockquote
cite="mid:1607364c.2c12.12f94a82c2d.Coremail.ptf1242@163.com"
type="cite">
<pre> constraints = none
constraint-algorithm = Lincs
</pre>
<br>
<br>
I saw my .log file. <br>
<br>
Input Parameters:<br>
integrator = md<br>
nsteps = 10000<br>
init_step = 0<br>
ns_type = Grid<br>
nstlist = 5<br>
ndelta = 2<br>
nstcomm = 1<br>
comm_mode = Linear<br>
nstlog = 50<br>
nstxout = 0<br>
nstvout = 0<br>
nstfout = 0<br>
nstenergy = 50<br>
nstxtcout = 50<br>
init_t = 0<br>
delta_t = 0.002<br>
xtcprec = 1000<br>
nkx = 0<br>
nky = 0<br>
nkz = 0<br>
pme_order = 4<br>
ewald_rtol = 1e-05<br>
ewald_geometry = 0<br>
epsilon_surface = 0<br>
optimize_fft = FALSE<br>
ePBC = xyz<br>
bPeriodicMols = FALSE<br>
bContinuation = FALSE<br>
bShakeSOR = FALSE<br>
etc = Berendsen<br>
epc = Berendsen<br>
epctype = Isotropic<br>
tau_p = 0.5<br>
ref_p (3x3):<br>
ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}<br>
ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}<br>
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}<br>
compress (3x3):<br>
compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}<br>
compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}<br>
compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}<br>
refcoord_scaling = No<br>
posres_com (3):<br>
posres_com[0]= 0.00000e+00<br>
posres_com[1]= 0.00000e+00<br>
posres_com[2]= 0.00000e+00<br>
posres_comB (3):<br>
posres_comB[0]= 0.00000e+00<br>
posres_comB[1]= 0.00000e+00<br>
posres_comB[2]= 0.00000e+00<br>
andersen_seed = 815131<br>
rlist = 0.9<br>
rtpi = 0.05<br>
coulombtype = Cut-off<br>
rcoulomb_switch = 0<br>
rcoulomb = 0.9Input Parameters:<br>
integrator = md<br>
nsteps = 10000<br>
init_step = 0<br>
ns_type = Grid<br>
nstlist = 5<br>
ndelta = 2<br>
nstcomm = 1<br>
comm_mode = Linear<br>
nstlog = 50<br>
nstxout = 0<br>
nstvout = 0<br>
nstfout = 0<br>
nstenergy = 50<br>
nstxtcout = 50<br>
init_t = 0<br>
delta_t = 0.002<br>
xtcprec = 1000<br>
nkx = 0<br>
nky = 0<br>
nkz = 0<br>
pme_order = 4<br>
ewald_rtol = 1e-05<br>
ewald_geometry = 0<br>
epsilon_surface = 0<br>
optimize_fft = FALSE<br>
ePBC = xyz<br>
bPeriodicMols = FALSE<br>
bContinuation = FALSE<br>
bShakeSOR = FALSE<br>
etc = Berendsen<br>
epc = Berendsen<br>
epctype = Isotropic<br>
tau_p = 0.5<br>
ref_p (3x3):<br>
ref_p[ 0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00}<br>
ref_p[ 1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00}<br>
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 1.00000e+00}<br>
compress (3x3):<br>
compress[ 0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00}<br>
compress[ 1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00}<br>
compress[ 2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05}<br>
refcoord_scaling = No<br>
posres_com (3):<br>
posres_com[0]= 0.00000e+00<br>
posres_com[1]= 0.00000e+00<br>
posres_com[2]= 0.00000e+00<br>
posres_comB (3):<br>
posres_comB[0]= 0.00000e+00<br>
posres_comB[1]= 0.00000e+00<br>
posres_comB[2]= 0.00000e+00<br>
andersen_seed = 815131<br>
vdwtype = Cut-off<br>
rvdw_switch = 0<br>
rvdw = 0.9<br>
epsilon_r = 1<br>
epsilon_rf = 1<br>
tabext = 1<br>
implicit_solvent = No<br>
gb_algorithm = Still<br>
gb_epsilon_solvent = 80<br>
nstgbradii = 1<br>
rgbradii = 2<br>
gb_saltconc = 0<br>
gb_obc_alpha = 1<br>
gb_obc_beta = 0.8<br>
gb_obc_gamma = 4.85<br>
sa_surface_tension = 2.092<br>
DispCorr = EnerPres<br>
free_energy = no<br>
init_lambda = 0<br>
sc_alpha = 0<br>
sc_power = 0<br>
sc_sigma = 0.3<br>
delta_lambda = 0<br>
nwall = 0<br>
wall_type = 9-3<br>
wall_atomtype[0] = -1<br>
wall_atomtype[1] = -1<br>
wall_density[0] = 0<br>
wall_density[1] = 0<br>
wall_ewald_zfac = 3<br>
pull = no<br>
disre = No<br>
disre_weighting = Conservative<br>
disre_mixed = FALSE<br>
dr_fc = 1000<br>
dr_tau = 0<br>
nstdisreout = 100<br>
orires_fc = 0<br>
orires_tau = 0<br>
nstorireout = 100<br>
dihre-fc = 1000<br>
em_stepsize = 0.01<br>
em_tol = 100<br>
niter = 20<br>
fc_stepsize = 0<br>
nstcgsteep = 1000<br>
nbfgscorr = 10<br>
ConstAlg = Lincs<br>
shake_tol = 0.0001<br>
lincs_order = 4<br>
lincs_warnangle = 30<br>
lincs_iter = 1<br>
bd_fric = 0<br>
ld_seed = 1993<br>
cos_accel = 0<br>
deform (3x3):<br>
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}<br>
userint1 = 0<br>
userint2 = 0<br>
userint3 = 0<br>
userint4 = 0<br>
userreal1 = 0<br>
userreal2 = 0<br>
userreal3 = 0<br>
userreal4 = 0<br>
grpopts:<br>
nrdf: 1941<br>
ref_t: 300<br>
tau_t: 0.1<br>
anneal: No<br>
ann_npoints: 0<br>
acc: 0 0 0<br>
nfreeze: N N N<br>
energygrp_flags[ 0]: 0<br>
efield-x:<br>
n = 0<br>
efield-xt:<br>
n = 0<br>
efield-y:<br>
n = 0<br>
efield-yt:<br>
n = 0<br>
efield-z:<br>
n = 0<br>
efield-zt:<br>
n = 0<br>
bQMMM = FALSE<br>
QMconstraints = 0<br>
QMMMscheme = 0<br>
scalefactor = 1<br>
qm_opts:<br>
ngQM = 0<br>
Table routines are used for coulomb: FALSE<br>
Table routines are used for vdw: FALSE<br>
Cut-off's: NS: 0.9 Coulomb: 0.9 LJ: 0.9<br>
System total charge: 0.000<br>
<br>
Enabling SPC water optimization for 216 molecules.<br>
<br>
Configuring nonbonded kernels...<br>
Testing AMD 3DNow support... not present.<br>
Testing ia32 SSE support... present.<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
However if i <br>
<pre>define =
constraints = none
constraint-algorithm = Lincs
The .log file is similar to the above .log file. So i can not know whether the constraints invoked.
</pre>
</blockquote>
<br>
I think you haven't looked far enough. Algorithms being used that
are important enough to have names and literature citations are
referred to by those in the .log file. Read and learn :-)<br>
<br>
<blockquote
cite="mid:1607364c.2c12.12f94a82c2d.Coremail.ptf1242@163.com"
type="cite">
<pre>
Is it only SETTLE algorithm for water models in Gromacs 4.5.3? </pre>
</blockquote>
<br>
Have you looked in the manual?<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:1607364c.2c12.12f94a82c2d.Coremail.ptf1242@163.com"
type="cite">
<pre>
>
>
>MD wrote:
>> Hi gromacs experts,
>>
>> I used gromacs 4.5.3. my system has only spce water, no other types.
>>
>> In .mdp file,
>>
>> I used the following parameters;
>>
>> define =
>>
>> constraints = none
>> constraint-algorithm = Lincs
>>
>> Can u tell me Is it flexible water or all the bond, angle fixed using
>> the above setting?
>>
>
>Look at spce.itp and/or your md.log file. If the #ifdef FLEXIBLE statement is
>not invoked, the SETTLE algorithm is used.
>
>>
>> what is the equations of potential energy in Gromacs 4.5 using OPLSAA?
>>
>
>The components of various functional forms are described in the manual.
>
>-Justin
>
>>
>> Best regards
>>
</pre>
<br>
<br>
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