Thanks. I am not interested in the real physics of the freezegroups as I am
assuming the fluctuations are negligible in the timescale of the
fluctuations of the non-freeze groups. I thought that the langevin
thermostat is quite effective in this case just to ensure that there is no
net heat flow fr
On Wed, Aug 21, 2013 at 10:22 PM, HANNIBAL LECTER
wrote:
> I am not sure what is the problem with using NPT, constraints and
> freezegroups. Unless there is some fundamental issue (which I cannot think
> of) one should in principle be able to run NPT with the CNT system by
> freezing the CNT group
OP, I give you 10/10. First time I laugh out loud reading the GMX mailing
list.
/J
On Wed, Aug 21, 2013 at 5:05 AM, Arunima Shilpi wrote:
> Dear Sir
> I have to query as to how do we convert the paramaters in "nm" to Å
> --. For example the RMSD and RMSF calculation gives result in "nm". I wa
On 8/21/13 4:22 PM, HANNIBAL LECTER wrote:
I am not sure what is the problem with using NPT, constraints and
freezegroups. Unless there is some fundamental issue (which I cannot think
of) one should in principle be able to run NPT with the CNT system by
freezing the CNT group. I am using sd wit
Dear Justin,
Thanks so much. If get stuck i will come knocking on your door.
Cheers.
On Wed, Aug 21, 2013 at 10:17 PM, Justin Lemkul wrote:
>
>
> On 8/21/13 4:00 PM, MUSYOKA THOMMAS wrote:
>
>> Dear users,
>> I am new to GROMACS and i have just been practising with several
>> tutorials.
>> I a
I am not sure what is the problem with using NPT, constraints and
freezegroups. Unless there is some fundamental issue (which I cannot think
of) one should in principle be able to run NPT with the CNT system by
freezing the CNT group. I am using sd with LINCS to constraint the bonds.
However, if md
On 8/21/13 4:00 PM, MUSYOKA THOMMAS wrote:
Dear users,
I am new to GROMACS and i have just been practising with several tutorials.
I am trying to do a molecular dynamics simulation of cysteine proteases an
example falcipain-2 (PDBID=2OUL) and got several issues to pose
1) looking at the structu
Dear users,
I am new to GROMACS and i have just been practising with several tutorials.
I am trying to do a molecular dynamics simulation of cysteine proteases an
example falcipain-2 (PDBID=2OUL) and got several issues to pose
1) looking at the structure it has water molecules - do i get rid of the
... which is why simplifying your predicate would have helped you
identify which part was wrong. Once you actually try
close = name "T3P";
close
and see that you get no atoms, your error becomes much easier to see!
Also faster than emailing ;-)
Mark
On Wed, Aug 21, 2013 at 4:46 PM, Albert wrot
On 08/21/2013 05:06 PM, Justin Lemkul wrote:
Your selection, as Teemu says, is calling for *atoms* named T3P that
are also *atoms* named O, which is clearly impossible. The *residue*
name is T3P.
-Justin
I see. thanks a lot for clearly pointing out. I changed it into
resname T3P
and it
On 8/21/13 11:02 AM, Albert wrote:
but actually the water name in my system IS "T3P" and the atom name in the water
model is "O". I've double checked for this.
Your selection, as Teemu says, is calling for *atoms* named T3P that are also
*atoms* named O, which is clearly impossible. The *r
but actually the water name in my system IS "T3P" and the atom name in
the water model is "O". I've double checked for this.
thx
Albert
On 08/21/2013 04:59 PM, Teemu Murtola wrote:
If that is really your selection, you are trying to select atoms that have
both name T3P and O, which is clearly
If that is really your selection, you are trying to select atoms that have
both name T3P and O, which is clearly impossible, so nothing gets selected.
Best regards,
Teemu
On Aug 21, 2013 5:13 PM, "Albert" wrote:
> Hello:
>
> I am trying to calculate the number of water molecules within 3 A of a
Hello Mark:
thanks for kind advices.
I checked my residues number carefully, and I didn't find anything
wrong. However, I am not sure whether the syntax of my selection.dat is
all right or not, since the documentation for this option is not well
clarified.
thank you very much
Albert
On
Simplify your condition gradually and find out which bit is wrong!
Mark
On Wed, Aug 21, 2013 at 4:13 PM, Albert wrote:
> Hello:
>
> I am trying to calculate the number of water molecules within 3 A of a
> resid 51, and here is my command:
>
> g_select -f md.xtc -s input.pdb -os water.xvg -sf se
Hello:
I am trying to calculate the number of water molecules within 3 A of a
resid 51, and here is my command:
g_select -f md.xtc -s input.pdb -os water.xvg -sf selection.dat
here is my selection.dat:
waterO = name "T3P" and name O;
close = waterO and within 0.3 of resnr 51;
close
the com
You can't take an OHN out of the coordinate file and not out of the
topology and produce a .tpr. Production of a .tpr requires that the
[molecules] field matches the coordinate file.
When you do have a .tpr, you are looking at *moltype*. This is the
internal representation of the [moleculetype]. I
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