You mean TMD (Targeted Molecular Dynamics). As far as I know, this is not
implemented in GROMACS (hope anyone corrects me if I am wrong)
2012/6/4 Mike M
> Dear Gromacs Users,
>
> I am trying to study the conformational path from state A to state B with
> targeted molecular dynamics. These two
Hi all,
When calculating the average number of hbonds during a simulation, does the
program g_hbond contemplate the possibility of an atom involved in two
hbond?
If I visualize the structures with molden, setting the same cutoff
criterion for hbonding than g_hbond utilizes, I found out that some O
Hi all,
When calculating the average number of hbonds during a simulation, does the
program g_hbond contemplate the possibility of an atom involved in two
hbond?
If I visualize the structures with molden, setting the same cutoff
criterion for hbonding than g_hbond utilizes, I found out that some O
1/11/13 6:23 AM, Miguel Ángel Mompeán García wrote:
>> Hi all,
>>
>> When calculating the average number of hbonds during a simulation, does
>> the
>> program g_hbond contemplate the possibility of an atom involved in two
>> hbond?
>> If I visualize
I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got:
dssp cmd='/usr/local/bin/dssp/ -i ddQ3PqtX -o ddR1HavD > /dev/null 2>
/dev/null'
Reading frame 0 time0.000
Back Off! I just backed up ddQ3PqtX to ./#ddQ3PqtX.1#
---
Dear gmx users,
Has anyone tried dssp-2.1.0 with gromacs-4.6?
I am having the common problems that were supossed not to be in the new
releases
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ens if you execute the command (/usr/local/bin/dssp/ -i ddQ3PqtX
> -o ddR1HavD) in your terminal?
>
>
> Erik
>
> On Mar 1, 2013, at 1:06 PM, Miguel Ángel Mompeán García wrote:
>
> I am using gromacs 4.6 and dssp-2.1.0 and I am getting that error you got:
>>
>> dss
for your comments
2013/3/1 Erik Marklund
> Interesting. Perhaps there are new issues with 2.1.0. Did you try to
> execute the command yourself?
>
> Erik
>
>
> On Mar 1, 2013, at 5:16 PM, Miguel Ángel Mompeán García wrote:
>
> The issue I mentioned was with dssp-2.1.0.
Dear gmx users,
I have successfully performed simulations on a charged peptide. I did a
series of mutations and everything had a happy end. Now I have tried
another mutation (just substitution of Asn to Lys) and I am getting the
well-known
"X particles communicated to PME node Y are more than a c
I have tried the same issue (same system with same mdp file and same
initial configuration as starting structure) and is running without
any problems with GROMACS-4.5.5.
Anyone knows what is happening?
2013/3/4, Justin Lemkul :
>
>
> On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote
The version I was using this morning was 4.6
2013/3/4, Justin Lemkul :
>
>
> On 3/4/13 3:08 PM, Miguel Ángel Mompeán García wrote:
>> I have tried the same issue (same system with same mdp file and same
>> initial configuration as starting structure) and is running without
omb= 1.0
rvdw= 1.0
pbc = xyz
Thank-you a lot for all your tips and comments,
Miguel
>
>
> -Justin
>
> 2013/3/4, Justin Lemkul :
>>
>>>
>>>
>>> On 3/4/13 3:08 PM, Miguel Ángel Mompeán García wrote:
>>>
>>>&
Dear all,
I am doing PCA on a 110ns run.
When calculating the subspace overlap from independent PCA performed in
different time windows, I expect the overlap to be 1 only when the time
interval is equal to 110ns, since both covariance matrices are identical.
However, I found that from the interval
Dear all,
I posted some days ago an issue regarding overlap values. If any of you is
experienced with this I would appreciate some comments. Please find below
the mentioned post:
I am doing PCA on a 110ns run.
When calculating the subspace overlap from independent PCA performed in
different time
after 70 ns doesn't contribute significantly to
> the covariance matrix anymore.
>
> Hope it helps,
>
> Tsjerk
>
>
>
> On Thu, May 30, 2013 at 12:26 PM, Miguel Ángel Mompeán García <
> mig.momp...@gmail.com> wrote:
>
> > Dear all,
> >
>
Dear gmx users,
Something very weird is happening with a .gro file and I wonder if any user
has ever experienced something similar...
I am doing umbrella sampling simulation on a peptide with capped termini
residues (ACE and NH2). As starting structure for the pulling simulations I
used the last
varying the starting point of the analysis, rather than the
> end point.
>
>
> Hope it helps,
>
> Tsjerk
>
>
> On Thu, May 30, 2013 at 1:37 PM, Miguel Ángel Mompeán García <
> mig.momp...@gmail.com> wrote:
>
> > Hi Tsjerk,
> >
> > Thanks
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