aiswarya pawar wrote:
I get an error like this=
Step 43230, time 86.46 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.033583, max 1.621884 (between atoms 2032 and 2030)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
I get an error like this=
Step 43230, time 86.46 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.033583, max 1.621884 (between atoms 2032 and 2030)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2032 2030 90.00.44
On 19/12/2011 1:05 AM, aiswarya pawar wrote:
Hi users,
I did energy minimization of a protein complex using the following
minimization mdp file.
See
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
for general advice.
; Lines starting with ';' ARE COMMENTS
; Ev
Hi users,
I did energy minimization of a protein complex using the following
minimization mdp file.
; Lines starting with ';' ARE COMMENTS
; Everything following ';' is also comment
title = Energy Minimization ; Title of run
; The following line tell the program the standard locations where to
On 4/30/2011 9:06 AM, Juliette N. wrote:
Dear experts,
I just tried the command mpirun -np 4 mdrun on 4.5.4 but after a few
steps I get LINCS error:
step 400, will finish Sat Apr 30 05:20:45 2011
Step 750, time 1.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 10.116560,
Dear experts,
I just tried the command mpirun -np 4 mdrun on 4.5.4 but after a few steps
I get LINCS error:
step 400, will finish Sat Apr 30 05:20:45 2011
Step 750, time 1.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 10.116560, max 72.359520 (between atoms 314 and 315)
bo
Yongchul Chung wrote:
After EM, I got:
Potential Energy = 1.7242092e+05
Maximum force = 2.1079963e+03 on atom 675
Norm of force = 5.9417034e+01
I think my system size is too big compared to the box size so I am going
to run the simulation with smaller number of molecules to see w
After EM, I got:
Potential Energy = 1.7242092e+05
Maximum force = 2.1079963e+03 on atom 675
Norm of force = 5.9417034e+01
I think my system size is too big compared to the box size so I am going to
run the simulation with smaller number of molecules to see whether this
helps or not.
Yongchul Chung wrote:
yes I carried out energy minimization and used following parameters.
OK, so what values of potential energy and maximum force did EM achieve?
-Justin
title = FWS
cpp = /usr/bin/cpp ; the c pre-processor
define = -DFLEXIB
Yongchul Chung wrote:
Hi again gmx-users,
I ran into LINCS error again when I tried to incorporate pressure
scaling parameters.
It seems like the initial pressure and temperature is erroneously large
as shown in the md.log file below. can anyone tell me how to fix this?
Did you run energ
Yongchul Chung wrote:
Hi guys,
As Justin pointed out, it was the problem with md simulation blowing up.
I also had coloumbtype=PME and had to switch to cut-off to make my
simulation run faster.
And it will be substantially less accurate than using PME. I would say Jochen's
advice is th
Hi guys,
As Justin pointed out, it was the problem with md simulation blowing up. I
also had coloumbtype=PME and had to switch to cut-off to make my simulation
run faster.
Thanks for all the help.
On Thu, Oct 8, 2009 at 11:44 AM, Jochen Hub wrote:
>
>
>
> delta_t = 0.01
>
> You a
delta_t = 0.01
You are using a 10 fs timestep!!! That is way too long. Standard is 2
(with bond constraints).
Yongchul Chung wrote:
Hi all,
I am trying to simulate 100 molecules of n-alkane molecules but keep
receiving LINC errors.
When I completed steepest descent I re
Yongchul Chung wrote:
Hi all,
I am trying to simulate 100 molecules of n-alkane molecules but keep
receiving LINC errors.
When I completed steepest descent I received following msg:
Steepest Descents converged to Fmax < 500 in 819 steps
Potential Energy = 1.7174361e+05
Maximum force =
Hi all,
I am trying to simulate 100 molecules of n-alkane molecules but keep
receiving LINC errors.
When I completed steepest descent I received following msg:
Steepest Descents converged to Fmax < 500 in 819 steps
Potential Energy = 1.7174361e+05
Maximum force = 4.4903098e+02 on atom 172
sarbani chattopadhyay wrote:
Hi,
I am trying to simulate a peptide whose structure is yet to be
validated experimentally.
It has 3 protonated lysine residues.
I have used "oplsaa" force filed with "spc" water model and had added 3
CL ions into the box.
Everything works fine till energ
Hi,
I am trying to simulate a peptide whose structure is yet to be validated
experimentally.
It has 3 protonated lysine residues.
I have used "oplsaa" force filed with "spc" water model and had added 3 CL ions
into the box.
Everything works fine till energy minimisation but after that du
Why don't you do energy minimization? It's pretty clear that you've generated
some atomic overlap in your procedure, from what you've described.
For general reference on such problems, check the hundreds of related posts
(LINCS warnings) in the list archive or the following link to the wiki site
Dear users,
I have a problem on running MD of 146 LC molecules system. I do not do the energy minimisation. I use NVT ensemble to equilibrate my system. My topology was created using PRODRG beta server. After the creation of my systems box (on top of each other)
1. editconf -f lc -bt d -box 1.3 0
This is an issue that has been discussed a lot on the list. The typical reasons
for LINCS errors can be found here:
http://wiki.gromacs.org/index.php/Errors#LINCS_warnings
Quoting vijay kumar hinge vijay <[EMAIL PROTECTED]>:
> hello users,
>
> i am using gromacs 3.3 version on unix platform
> i
hello users,
i am using gromacs 3.3 version on unix platform
i got these error while running MD simulation of 89 aa in spc216 water for
10ns at step 4088373 time 8176.55 .i had used force field 4a1(official
distribution)
hear I'm sending .mdp file also
error which i got is
--
Mark Abraham a écrit :
Dear GROMACS users,
I am trying to run md of a protein with a non-standard residue.
It was fine up until I ran mdrun with pr.mdp, where I received a LINCS
warning after 20 steps (0.042 ps).
Step 21, time 0.042 (ps) LINCS WARNING
I looked up the mailing list and
Hi Shangwa Han,
First of all, there is no general conclusion regarding such error.
Second, the general conclusion is: your system contains severe errors,
which have not been resolved during energy minimization, if you
performed any, but you didn't mention it.
If you would have browsed the archiv
> Dear GROMACS users,
>
>
>
> I am trying to run md of a protein with a non-standard residue.
>
> It was fine up until I ran mdrun with pr.mdp, where I received a LINCS
> warning after 20 steps (0.042 ps).
>
>
>
> Step 21, time 0.042 (ps) LINCS WARNING
> I looked up the mailing list and found dis
Dear GROMACS users,
I am trying to run md of a protein with a non-standard residue.
It was fine up until I ran mdrun with pr.mdp, where I received a LINCS
warning after 20 steps (0.042 ps).
Step 21, time 0.042 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 23696503603
Hi!
this is my problem: after a few step (from 1 to 20) mdrun stops because
of lincs
"...LINCS WARNING - Relative constraint deviation after lincs: max
103.684275 (between atoms 7941 and 7942) rms 1.227871 bonds that rotated
more than 180 degrees..."
7941 e 7942 should be two water atoms
Dear all,
I have been trying to simulate various mutant models (single
mutant) of a enzyme. I am successfully finished simulation of 3
variants including wild type (So for finished up to position
restraints of all variants). In one mutation involving "Ala" in
requsite
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