Mr Justin:
I have tried to do energy minimization in this situation which only existing
small molecule in water, I found the structure of organic molecule didn’t
become distortions. I think the distortions of organic molecules are due to
these stronger interactions between small molecules
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On 8/4/17 4:42 AM, yujie liu wrote:
Hello, users
I’m a novice to study the gromacs program. Now I met some problems which the small molecule occurred deformation when energy minimization was performed. For example, the anthracene molecule became bent in the plane of C-rings, the same as
On 8/4/17 4:57 AM, G R wrote:
Dear users,
I try to implement Clayff forcefield for Kaolinite. I created my force
field (I'm not sure about it), but gromacs couldn't find my force field in
the directory. Here is my forcefield.
ffnonbonded
[ atomtypes ]
; name mass chargeptype
On 8/4/17 11:13 AM, farial tavakoli wrote:
blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px
#715FFA solid !important; padding-left:1ex !important; background-color:white
!important; } Dear gromacs user
I am performing protein ligand complex (t4lysosim) and now i
On 8/5/17 8:12 AM, Mahsa E wrote:
Dear gmx-users,
I am trying to build a polymer box from scratch and generate the required
input files. So far, I did these steps:
1. built a chain of the polymer
2. run ACPYPE to generate the topology file...
However, since the chain is long, it took so long
On 8/5/17 8:12 PM, Mark Abraham wrote:
Hi,
I'd start by checking if that last residue is a normal one...
The check_oo() function in gmx_do_dssp.cpp looks like it will not work correclty
for CHARMM, because it does not identify CHARMM termini, thereby ignoring the
C-terminus. It looks
Hi,
This a question you should answer with the online documentation for your
cluster.
Mark
On Sat, Aug 5, 2017 at 4:28 PM Neha Gupta wrote:
> Hi gromacs users,
>
> I use cygwin terminal in windows 7, 64 bit computer.
>
> How to use qsub commands and thereby do gromacs
Hi,
I'd start by checking if that last residue is a normal one...
Mark
On Sat, Aug 5, 2017 at 2:02 PM YanhuaOuyang <15901283...@163.com> wrote:
>
>
> Dear Mark,
>
>Thank you, I have figure out the problem, but to my surprise, the
> output xpm file lack the information of the last residue
Hello,
will decouple intramuscular interactions during windows simulation impact
the accuracy of the PME estimated?
I am pulling large molecule
Regards
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Hi gromacs users,
I use cygwin terminal in windows 7, 64 bit computer.
How to use qsub commands and thereby do gromacs simulations in a cluster?
Can anyone tell me clearly?
Thanks,
Neha
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Dear gmx-users,
I am trying to build a polymer box from scratch and generate the required
input files. So far, I did these steps:
1. built a chain of the polymer
2. run ACPYPE to generate the topology file...
However, since the chain is long, it took so long time with ACPYPE and the
calculation
Dear gmx-users,
I am trying to build a polymer box from scratch and generate the required
input files. So far, I did these steps:
1. built a chain of the polymer
2. run ACPYPE to generate the topology file...
However, since the chain is long, it took so long time with ACPYPE and the
calculation
Hi,
I have installed 5.1.1, and am trying to run the simulations. During the
run, I am getting this error as pasted below:
WARNING: Listed nonbonded interaction between particles 1 and 9
at distance 9.500 which is larger than the table limit 2.030 nm.
This is likely either a 1,4 interaction, or
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