c***r
发帖数: 4631 | 1 hi, is there anybody familiar with Gromacs?
is it powerful enough to simulate large molecules? |
d*****w
发帖数: 124 | 2 我一直在用DLPOLY, 但有同事向我强烈推荐GROMACS,前几天我就装上试了一下
几句简单的评述在这里:
http://pplas.icas.ac.cn/bbs/topic.cgi?forum=5&topic=2&show=0
【在 c***r 的大作中提到】
: hi, is there anybody familiar with Gromacs?
: is it powerful enough to simulate large molecules?
|
b*******u
发帖数: 62 | 3 it is very quick based on the assumption
you will use all the default they set etc.
like timestep 7fs instead of 2fs in most
literature. otherwise it will not be that
quick.
【在 c***r 的大作中提到】
: hi, is there anybody familiar with Gromacs?
: is it powerful enough to simulate large molecules?
|
j*x
发帖数: 302 | 4 another comment on gromacs is that it is not good for some protein
systems although the initial motivation of this program is (partly) for
protein and DNA. The reason is that they don't have multiple-timestep
scheme. Actually they didn't like MTS so that they didn't implement it.
For highly charged protein systems, it becomes a problem in long simulations.
looks like many people just ignore it, or maybe people didn't run
simulations over 10 ns very frequently.
【在 b*******u 的大作中提到】
: it is very quick based on the assumption
: you will use all the default they set etc.
: like timestep 7fs instead of 2fs in most
: literature. otherwise it will not be that
: quick.
|
b*******u
发帖数: 62 | 5 but i thought multiple-timestep is for time-saving.
what is the relation with the stability of the simulation?
【在 j*x 的大作中提到】
: another comment on gromacs is that it is not good for some protein
: systems although the initial motivation of this program is (partly) for
: protein and DNA. The reason is that they don't have multiple-timestep
: scheme. Actually they didn't like MTS so that they didn't implement it.
: For highly charged protein systems, it becomes a problem in long simulations.
: looks like many people just ignore it, or maybe people didn't run
: simulations over 10 ns very frequently.
|
