Dear users,
If I obtain/generate the topology file for a ligand using another program
(except PRODRG);
1) How can I arrange .itp file? Because it seems very complicate.
2) Justin tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
We will make
On 23/09/2011 4:37 PM, Sumanth M. Kumar wrote:
Hi everyone,
I did a simulation in an amazon cluster with 7.5 GB memory and 4 EC2
Compute Units (2 virtual cores with 2 EC2 Compute Units each) and it
was done with 0.5ns/day. Now Im running a simulation in another amazon
cluster of 7 GB of memory
Hi everyone,
I did a simulation in an amazon cluster with 7.5 GB memory and 4 EC2 Compute
Units (2 virtual cores with 2 EC2 Compute Units each) and it was done with
0.5ns/day. Now Im running a simulation in another amazon cluster of 7 GB of
memory and 20 EC2 Compute Units (8 virtual cores with 2.5
g_sas -oa
...
Tsjerk
On Sep 22, 2011 9:35 AM, "aiswarya pawar" wrote:
Hi users,
what are options for obtaining the surface atoms exposed to solvent, i need
the list of these atoms.
Thanks
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2011/9/23 Víctor Bahamonde
> Hello gmx users
>
> I have a question related to gromacs compilation
> in the same machine, are there any difference in the result of MD when I
> compile the same version of gromacs but with diferent version of gcc?
> also, gcc 4.1.x still broken?
> I use Debian 5 a
On 23/09/2011 10:19 AM, Víctor Bahamonde wrote:
Hello gmx users
I have a question related to gromacs compilation
in the same machine, are there any difference in the result of MD
when I compile the same version of gromacs but with diferent version
of gcc?
Yes, MD systems are chaotic. The ti
Hello gmx users
I have a question related to gromacs compilationin the same machine, are there
any difference in the result of MD when I compile the same version of gromacs
but with diferent version of gcc?also, gcc 4.1.x still broken?I use Debian 5
and Debian 6 on amd phenom II quad core.
Tha
On 23/09/2011 2:04 AM, Jinan Niu wrote:
Hi, Mark:
Thanks for your reply.
my configure line is just simple :
./configure --prefix=/home/njn/zms/1gmx4.5.5 --enable-mpi
this would cause the following error:
--
aiswarya.pa...@gmail.com wrote:
Hi users,
Am using g_mindist to calculate the distances. Now I have to calculate for each
atom ie around 1000atoms. If I try running this command in a shell script, how
would designate the index file, ie my index file has protein atoms and water
atoms, and ha
Hi users,
Am using g_mindist to calculate the distances. Now I have to calculate for each
atom ie around 1000atoms. If I try running this command in a shell script, how
would designate the index file, ie my index file has protein atoms and water
atoms, and have to find distance between one prot
Hi, Mark:
Thanks for your reply.
my configure line is just simple :
./configure --prefix=/home/njn/zms/1gmx4.5.5 --enable-mpi
this would cause the following error:
---
..
checking size of off_
ahmet yıldırım wrote:
Dear Justin,
If possible, can you some explain "net attraction"?
Forces are either attractive or repulsive. "Net attraction" means attractive
forces dominate over repulsive ones. Please consult some elementary physics or
chemistry textbooks for more on these concep
Dear Justin,
If possible, can you some explain "net attraction"?
Best regards
2011/9/22 Justin A. Lemkul
>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>>
>> 1.) During the simulation the mean potential energy is minus (-) value.
>> What does this mean? Why minus?
>>
>
> Net attraction.
>
>
> 2
Ehud Schreiber wrote:
Hi,
I’m currently utilizing gromacs using the opls-aa forcefield in an
implicit-solvent setting.
Can any of the developers roughly predict in what version, and when,
will GPU acceleration be applicable for such work? I am afraid the
gromacs 4.6 roadmap webpage lef
Hi,
I'm currently utilizing gromacs using the opls-aa forcefield in an
implicit-solvent setting.
Can any of the developers roughly predict in what version, and when,
will GPU acceleration be applicable for such work? I am afraid the
gromacs 4.6 roadmap webpage left me confused.
By the way, th
bob dole wrote:
Hello,
I have conducted several runs in which I pull one peptide away from
another; however, the peptide being pulled gets visually “stretched” out
when viewing the trajectory in VMD and DSSP confirms this. I came across
this recent post
(http://lists.gromacs.org/pipermail
Hello,
I
have conducted several runs in which I pull one peptide away from
another; however, the peptide being pulled gets visually “stretched”
out when viewing the trajectory in VMD and DSSP confirms this. I came
across this recent post
(http://lists.gromacs.org/pipermail/gmx-users/2011-Septembe
On Thu, Sep 22, 2011 at 8:11 PM, zhongjin wrote:
> The system is Rocks 4.3 (Mars Hill), and
> [hzj1000@ZhouGroup ~]$ rpm -aq |grep glibc
> glibc-kernheaders-2.4-9.1.100.EL
> glibc-2.3.4-2.36
> glibc-headers-2.3.4-2.36
> glibc-common-2.3.4-2.36
> glibc-devel-2.3.4-2.36
>
> [hzj1000@ZhouGroup ~]$ g
The system is Rocks 4.3 (Mars Hill), and
[hzj1000@ZhouGroup ~]$ rpm -aq |grep glibc
glibc-kernheaders-2.4-9.1.100.EL
glibc-2.3.4-2.36
glibc-headers-2.3.4-2.36
glibc-common-2.3.4-2.36
glibc-devel-2.3.4-2.36
[hzj1000@ZhouGroup ~]$ gcc -v
Reading specs from /usr/lib/gcc/i386-redhat-linux/3.4.6/spec
ahmet yıldırım wrote:
Dear Justin,
Thanks for your reply.
Tsjerk:
http://lists.gromacs.org/pipermail/gmx-users/2009-October/045884.html
There are two things to distinguish:
1. The reference structure used to remove translational and
rotational
degrees of free
Dear Justin,
Thanks for your reply.
Tsjerk:
http://lists.gromacs.org/pipermail/gmx-users/2009-October/045884.html
There are two things to distinguish:
>
> 1. The reference structure used to remove translational and rotational
> degrees of freedom
> 2. The reference against which the deviations (on
Hi GMXusers,
I know that the g_energy can be used to compute/estimate the adiabatic and
isothermal compressibility values of the simulation box when the TEMP, volume
and nmol values are given. nmol can be easily given for a pure solvent but when
I have a two (or more) different species in the m
Hi users,
what are options for obtaining the surface atoms exposed to solvent, i need
the list of these atoms.
Thanks
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/
Thanks Mark for your reply. First I want to know do I have to update GMX? for
example, when GMX4.5.5 come out, and I use GMX4.5.5 instead of GMX4.5.4. I
think GMX4.0.7 is even more stable.
Second is the error while install GMX4.5.5. I use configure instead of CMake.
I have successfully installe
Hi Tsjerk,
i used the command in format-
g_mindist -f md.xtc -s md.tpr -n 13.ndx -od 13.xvg -on 13.xvg -o 13.out -b
500 -e 1500 -d 0.5
so here i obtain the output-
atmpair.out-
0.00e+0013 21161
1.00e+0013 21161
2.00e+0013
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