<p class="MsoNormal"></p><p class="MsoNormal"></p><p class="MsoNormal"></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">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, </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">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"></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"></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>. </p>
<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></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></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><b></b></i>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></p><p></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>
<p></p>