<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
On 25/04/2012 6:28 AM, PAVAN PAYGHAN wrote:
<blockquote
cite="mid:CAJ0xtdHZ6Ca65Z2b4L4zTvN61KsjxDG_X1=RHFwTixJE57E2jA@mail.gmail.com"
type="cite">
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">Dear Gromacs
Users,</span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">I am
using gromacs version is 4.5.3.<span
class="apple-converted-space"> and running
my jobs </span>on single node with 8 cores.</span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222"><span
class="apple-converted-space">I
have two different systems which</span> contain about 425000
atoms (protein +
Lipid +SOL) one with bound ligand </span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">and another
one unbound protein.<span class="apple-converted-space"> </span>I
have successfully reached up to
NPT equilibration run step, <br>
</span></p>
</blockquote>
<br>
It is a poor idea to do equilibration with Parinello-Rahman, which
is unstable when the system is not already close to equilibrium. For
some reason people still do it, despite at least a post per week on
this list suggesting against it, and a warning in the manual. Use
Berendsen to fix the density, then equilibrate further with P-R to
get the right ensemble.<br>
<br>
<blockquote
cite="mid:CAJ0xtdHZ6Ca65Z2b4L4zTvN61KsjxDG_X1=RHFwTixJE57E2jA@mail.gmail.com"
type="cite">
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">now I want to
continue the same for production
run. Without ligand I am able to run successfully But the same
system with
ligand is crashing with following error-</span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">D D cell
1 0 0 could only obtain 1520 of the 1521 atoms that are</span> </p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">are </span><span
style="color:rgb(34,34,34);font-family:'Times New
Roman',serif;font-size:14pt;line-height:115%"> </span><span
style="color:rgb(34,34,34);font-family:'Times New
Roman',serif;font-size:14pt;line-height:115%">connected via
constraints from the
neighbouring cells</span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:115%;font-family:"Times
New Roman","serif";color:#222222">This probably
means your
constraint length are too long</span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">compared
to</span> <span style="color:rgb(34,34,34);font-family:'Times
New Roman',serif;font-size:14pt;line-height:115%">the domain
decomposition
cell size.</span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">Decrease
the number of domain decomposition grid cells or lincs_order</span>.
<br>
</p>
</blockquote>
<br>
I'd rather expect your system was blowing up because of the above
issue. Perhaps the suggestion in the error message is not as
complete as could be desired - you have so many atoms per processor
that the constraint length would normally be tiny with respect to
the cell size. So I think the things you have tried below are
rearranging the deck chairs on the Titanic.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAJ0xtdHZ6Ca65Z2b4L4zTvN61KsjxDG_X1=RHFwTixJE57E2jA@mail.gmail.com"
type="cite">
<span style=""></span>
<p class="MsoNormal" style="line-height:150%"><span
style="color:rgb(34,34,34);font-family:'Times New
Roman',serif;font-size:14pt;line-height:115%"> </span><span
style="color:rgb(34,34,34);font-family:'Times New
Roman',serif;font-size:14pt;line-height:150%">Accordingly
following the suggestions given in the error I tried to solve
it with</span></p>
<p class="MsoNormal" style="line-height:150%"><span
class="apple-converted-space"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">Following
log file and changed,</span></span></p>
<p class="MsoListParagraphCxSpFirst" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">1.<span
style="font-family:'Times New
Roman';font-size:7pt;line-height:normal"> </span></span>
<span style="color:rgb(34,34,34);font-family:'Times New
Roman',serif;font-size:19px;line-height:28px;text-indent:0px">1.
-rcon</span> </p>
<p class="MsoListParagraphCxSpFirst" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">
Estimated maximum distance required for p-lincs was 0.877 thus
I
increased it to 0.900</span></p>
<p class="MsoListParagraphCxSpLast" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222"> then it
thrown another error.</span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222"> The initial
cell size (0.877)
is smaller than the cell size limit (0.900)</span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222"><br>
</span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">2 .Then</span><span
style="color:rgb(34,34,34);font-family:'Times New
Roman',serif;font-size:14pt;line-height:150%"> I tried to
increase the –dds and –rdd from original values
of 1.25 and 0.623 to 1.30 and 0.670 respectively.</span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="color:rgb(34,34,34);font-family:'Times New
Roman',serif;font-size:14pt;line-height:150%"> But it does
not help </span><span
style="color:rgb(34,34,34);font-family:'Times New
Roman',serif;font-size:14pt;line-height:150%">and ended with
run crash.</span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222"> <i><b>What I
did was logical or I did it wrongly?</b></i></span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222"><i><b>Now can
anyone please suggest me the appropriate way to deal with
the problem mentioned
above? </b></i></span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">As I want
the continuation of the same run without altering the output
after change in
the parameters (As I have to compare the output with unbound
protein run thus can’t
afford change in output with change in parameters) </span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">I know
that I need to change some of the parameters in .mdp file such
as </span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">fourierspacing
from
0.16 to 0.12 and on the contrary increase the pme_order from
say 4 to 6.</span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222"><i><b>But as
asked above by doing so the output will not or will be the
exact continuation run?</b></i></span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222"><i><b>How to
increase the ratio of cell size to constrain length per
error message?</b></i></span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222"><i><b>If any
better way of doing so without changing the output please
suggest,</b></i></span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">I am
suffering from the same problem since long, </span></p>
<p class="MsoNormal" style="line-height:150%"><span
style="font-size:14.0pt;line-height:150%;font-family:"Times
New Roman","serif";color:#222222">Please
help me .Please see the mdp file for the reference.</span></p>
<p class="MsoNormal"><span class="apple-converted-space"><span
style="font-size:10.0pt;line-height:115%;font-family:"Times
New Roman","serif";color:#222222"> </span></span><span
style="font-size:10.0pt;line-height:115%;font-family:"Times
New Roman","serif";color:#222222">integrator
= md</span><br style="">
<br>
<span style="">nsteps
= 10000000</span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;line-height:115%;font-family:"Times
New Roman","serif";color:#222222"> dt
= 0.002
; 2 fs</span><br style="">
<span style="">> ></span><br style="">
<span style=""> ; Output
control</span><br style="">
<span style="">nstxout
= 1000
; <br>
nstvout
= 1000
; <br>
nstxtcout = 1000
;
</span></p>
<p class="MsoNormal"><span style="">nstenergy =
1000
;
</span></p>
<p class="MsoNormal"><span style=""> nstlog
= 1000
; <br>
; Bond parameters<br>
continuation = yes
; Restarting after NPT<br>
constraint_algorithm = lincs ; holonomic
constraints<br>
constraints = all-bonds
; all bonds (even heavy atom-H bonds)<br>
lincs_iter = 1
; accuracy of LINCS<br>
lincs_order = 4</span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;line-height:115%;font-family:"Times
New Roman","serif";color:#222222">;
Neighborsearching</span><br style="">
<span style="">ns_type = grid</span><br style="">
<span style="">nstlist
= 5</span> </p>
<p class="MsoNormal"> rlist = 1.2<br style="">
<span style="">rcoulomb = 1.2</span><br style="">
<span style="">rvdw
= 1.2</span><br style="">
<span style="">; Electrostatics</span><br style="">
<span style="">coulombtype = PME</span><br style="">
<span style="">pme_order = 4</span><br style="">
<span style="">fourierspacing
= 0.16</span>
<br style="">
<span style="">tcoupl
= Nose-Hoover</span><br style="">
<span style="">tc-grps
= Protein P
SOL_NA_CL ; <br>
tau_t
= 0.5 0.5 0.5<br>
ref_t
= 323 323 323
group, in K</span><br style="">
<span style="">; Pressure coupling is on</span><br style="">
<span style="">pcoupl =
Parrinello-Rahman ;
</span></p>
<p class="MsoNormal"><span style="">pcoupltype = semiisotropic
<br>
tau_p
= 2.0
; time<br>
ref_p
= 1.0 1.0
; reference<br>
compressibility = 4.5e-5
4.5e-5
; </span></p>
<p class="MsoNormal"><span style=""> ;
Periodic boundary conditions<br>
pbc
= xyz
; 3-D
PBC </span></p>
<p class="MsoNormal"><span style=""> ; Dispersion correction</span><br
style="">
<span style="">DispCorr = EnerPres
; account for cut-off vdW scheme</span> </p>
<p class="MsoNormal">; Velocity generation<br style="">
<span style=""> gen_vel
= no</span></p>
<p class="MsoNormal"><span
style="font-size:10.0pt;line-height:115%;font-family:"Times
New Roman","serif";color:#222222"> </span></p>
<p class="MsoNormal"><span
style="line-height:115%;font-family:'Times New
Roman',serif;color:rgb(34,34,34)"><font size="4"> </font></span></p>
<p class="MsoNormal"><span
style="line-height:115%;font-family:'Times New
Roman',serif;color:rgb(34,34,34)"><font size="4">Thanking in
Advance</font></span></p>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>