On 11/02/2012 4:15 AM, francesca vitalini wrote:
Ok now I have tryied to restart it all and the problem seems to be
that the system has some overlapping. In fact, no matter what I
freeze, water, CA or nothing, I get this error message
VERSION 3.3.1
This program is free software; you
On 11/02/2012 2:48 AM, francesca vitalini wrote:
In fact in the reverse transformation I'm feeding the CG structure
information.
Yes, but you need a source of atomistic intra-residue knowledge about
protein structure in order to convert a CG structure to something that
is vaguely plausible at
Ok now I have tryied to restart it all and the problem seems to be that the
system has some overlapping. In fact, no matter what I freeze, water, CA or
nothing, I get this error message
VERSION 3.3.1
This program is free software; you can redistribute it and/or
modify it under
In fact in the reverse transformation I'm feeding the CG structure
information.
Once I look through VMD to the FG structure I notice that the backbones are
not in planes so definitely I need to run some minimization there. In the
tutorial they were using simulating annealing, but I don't think I ne
On 11/02/2012 12:41 AM, francesca vitalini wrote:
In order to overcome the problem I tried to fix everything except the
backbone (solvent, sidechain and CA, as I want the structure to be
maintained). However, if I do then I have problems with the energy
minimization as the force on the 15300 is
In order to overcome the problem I tried to fix everything except the
backbone (solvent, sidechain and CA, as I want the structure to be
maintained). However, if I do then I have problems with the energy
minimization as the force on the 15300 is infinite.
Getting Loaded...
Reading file EM1-1.tpr,
francesca vitalini wrote:
I achieve
Steepest Descents converged to machine precision in 205 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.49131940478719e+07
Maximum force = 1.09664530279637e+06 on atom 1520(parto of the
protein)
Norm of force = 2.2836
I achieve
Steepest Descents converged to machine precision in 205 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -1.49131940478719e+07
Maximum force = 1.09664530279637e+06 on atom 1520(parto of the
protein)
Norm of force = 2.28369808518165e+06
and the system l
francesca vitalini wrote:
Tryed the double precision without any success... Again the same type of
error message. Might need to try other minimization algorithm. Any
suggestions on that?
What is the Fmax you achieve, and what are your intents for this process?
Minimizing very low is only
Tryed the double precision without any success... Again the same type of
error message. Might need to try other minimization algorithm. Any
suggestions on that?
2012/2/9 Justin A. Lemkul
>
>
> francesca vitalini wrote:
>
>> Hi all!
>> I'm trying to run some energy minimization with gromacs 3.3.1
francesca vitalini wrote:
Hi all!
I'm trying to run some energy minimization with gromacs 3.3.1 on a
system that I have transformed from cg to aa. After the reverse
transformation I solvate the system and I try to minimize just the
proteins (my system is a dimer) keeping fixed the water. The
Hi all!
I'm trying to run some energy minimization with gromacs 3.3.1 on a system
that I have transformed from cg to aa. After the reverse transformation I
solvate the system and I try to minimize just the proteins (my system is a
dimer) keeping fixed the water. Then the idea would be to minimize t
On 2011-05-21 09.09, sreelakshmi ramesh wrote:
Dear all,
I am using tabulated potential do simulate nacl in water
.when i was doing my energy minimization it gives me the following
error.Any help please..
Do you mean to say your table is correct?
Check the derivative numerically
Dear all,
I am using tabulated potential do simulate nacl in water .when i
was doing my energy minimization it gives me the following error.Any help
please..
WARNING: For the 1498 non-zero entries for table 2 in table_NA_CL.xvg the
forces deviate on average 39% from minus the numeri
Ok thanks
On Fri, Apr 15, 2011 at 9:56 PM, Justin A. Lemkul wrote:
>
>
> Kavyashree M wrote:
>
>> Dear gromacs users,
>>
>> While doing energy minimization for a protein (from pdb), with oplsaa
>> force field
>> and tip4p water model, there was an error and em stopped -
>>
>> Fatal error:
>> A c
Kavyashree M wrote:
Dear gromacs users,
While doing energy minimization for a protein (from pdb), with oplsaa
force field
and tip4p water model, there was an error and em stopped -
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your
Dear gromacs users,
While doing energy minimization for a protein (from pdb), with oplsaa force
field
and tip4p water model, there was an error and em stopped -
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilib
Thank you so much for all the helpful response.
On Wed, May 6, 2009 at 4:59 PM, Mark Abraham wrote:
> Yanmei Song wrote:
>
>> Dear All:
>>
>> I just installed the gmx_4.0.4 double precision.
>>
>> When I do EM, the grompp_d command has no problem. However after I submit
>> the job, it gives me t
Yanmei Song wrote:
Dear All:
I just installed the gmx_4.0.4 double precision.
When I do EM, the grompp_d command has no problem. However after I
submit the job, it gives me the following error. Anyone can tell me what
is the problem which may cause that?
You're using a new .tpr with an o
Justin A. Lemkul wrote:
Yanmei Song wrote:
Dear All:
I just installed the gmx_4.0.4 double precision.
When I do EM, the grompp_d command has no problem. However after I
submit the job, it gives me the following error. Anyone can tell me
what is the problem which may cause that? By the
Yanmei Song wrote:
Dear All:
I just installed the gmx_4.0.4 double precision.
When I do EM, the grompp_d command has no problem. However after I
submit the job, it gives me the following error. Anyone can tell me what
is the problem which may cause that? By the way, in 4.0.4, it can only
Dear All:
I just installed the gmx_4.0.4 double precision.
When I do EM, the grompp_d command has no problem. However after I submit
the job, it gives me the following error. Anyone can tell me what is the
problem which may cause that? By the way, in 4.0.4, it can only use 4 CPU,
right? Can we s
Check your trajectory to visually check whether it has exploded. This
may lead you to check all your input files, especially the mdp files.
This error may happen even in good settings, but Variable ci shall not
differ much from the desired range. In that case, I will turn Pressure
coupling off nd
hello,everyone
I am new of gromacs. I am running a sample following the Tutorial for Drug -
Enzyme Complex,which was written by John E.Kerrigan,Ph.D.
When I run the energy minimization ,it has error as followed.
Range checking error:
Explanation: During neighborsearching, we assign each particl
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