Re: [gmx-users] (no subject)

[Justin A. Lemkul]

JMandumpal wrote:
 
I think, setting tc groups = systemwill solve this issue.


Bad idea.  Treating the protein and the surrounding solvent together will lead
to temperature differences between the two groups, such that the overall system
will have the correct temperature, but the protein and solvent will be at
different temperatures - certainly non-physical!

There is a reason that grompp suggests using Protein/Non-Protein...

-Justin



On Thu, 17 Jul 2008 Justin A.Lemkul wrote :
 >For warnings/errors, etc. please check the archive and wiki before 
posting.  I just responded to a similar issue a few days ago:

 >
 >http://www.gromacs.org/pipermail/gmx-users/2008-June/034786.html
 >
 >-Justin
 >
 >[EMAIL PROTECTED] wrote:
 >>Hi all
 >>I have installed gromacs 3.3.3 in one of my 32 machine fedora core 2.
 >>so check i tried to to do speptide tutorial in
 >>/usr/local/gromacs/share/gromacs/tutor/speptide
 >>
 >>But when i m running grompp for position restraint with the command
 >>grompp -f pr -o pr -c after_em -r after_em -p speptide
 >>
 >>i get the following warning
 >>
 >>  WARNING 1 [file aminoacids.dat, line 1]:
 >>  T-Coupling group Protein has fewer than 10% of the atoms (191 out of
 >>  2741)
 >>  Maybe you want to try Protein and Non-Protein instead?
 >>
 >>I tried to change SOL with non protein but getting the same warning. 
is it

 >>ok to go further with this warning
 >>
 >>When i did grompp for full MD with the command
 >>
 >>grompp -v -f full -o full -c after_pr -p speptide
 >>
 >>again i m getting the same warning
 >>
 >>WARNING 1 [file aminoacids.dat, line 1]:
 >>  T-Coupling group Protein has fewer than 10% of the atoms (191 out of
 >>  2741)
 >>  Maybe you want to try Protein and Non-Protein instead?
 >>
 >>
 >>I tried to change SOL with non protein but getting the same warning.
 >>
 >>I don't know what to do now and how can i overcome this, if anyone could
 >>help me.
 >>
 >>Thanks
 >>
 >>ALKA



Rediff Shopping 





--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin




--


Justin A. Lemkul
Graduate Research Assistant
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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Re: [gmx-users] Using user-tables for simulations in vacuum

[David van der Spoel]

sapna sarupria wrote:

Hello,

The simulation does not run even for one step and therefore, it is not 
possible for me to check any of the components such as energy, 
temperature etc. There is no error message except for "segmentation 
fault". It does the same thing if I try to energy minimize the system 
instead of running an MD simulation. The corresponding mdp file is 
pasted below:

cpp=  /lib/cpp
constraints =  none
integrator   =  steep
nstcgsteep =  500
emtol =  500.0
emstep =  0.001
vdwtype=  user
energygrps  =  POL
energygrp_table =  POL POL

The commands I use are as follows:
grompp -f em.mdp -p 25mer_wca_vac.top -c 3.5ns.gro
mdrun -s topol.tpr -table table.xvg



Maybe you should make the table way longer. IIRC this is in vacuum with 
no cutoffs. Then the interactions should still fall within the length of 
the table.



Regards
Sapna


On Wed, Jul 16, 2008 at 10:08 AM, David van der Spoel 
<[EMAIL PROTECTED] > wrote:


sapna sarupria wrote:

Hello,

Thanks David for your response. Actually I have used the same
tables for simulations of the polymer in water and have had no
problem with them. Those simulations run for 4 ns without a
problem. So the tables are correct and I am sure of that. I am
not using the CVS version and so I give the energy and second
derivative in the table.  I have used user-defined tables in the
past and so the setup is correct in terms of changing the mdp
file and the top file. The problem seems to be more system
specific (meaning vacuum) than user error specific. Can you
suggest any other thing that may be the problem.

Have you checked energy components, temperature etc.?



Thanks a lot for your help.

Regards
Sapna


On Wed, Jul 16, 2008 at 9:23 AM, David van der Spoel
<[EMAIL PROTECTED] 
>> wrote:

   sapna sarupria wrote:



   -- Forwarded message --
   From: *sapna sarupria* <[EMAIL PROTECTED]

   >
   

   >