Dear Gromacs Users,
I noticed that quite often after adding the solvent (water) to the protein,
the water
molecules fill in gaps inside the protein which are not occupied.
I am afraid that since their position may not be optimal (they actually
should not
be there), it will lead to artifacts as the
Dear All,
I am facing an issue I do not fully understand. Namely, let's take two
crystallographic structures of the same protein and in one of them let's
delete three crystallographic water molecules that are not buried inside
the protein (let's forget about a reason for it for a moment).
Now, wh
Dear All,
I am using amber99fb-star-ildn with Gromacs2016.3 and I'm not sure how to
choose some options for non-bonded interactions such as
vdw-modifier (potential-shift or potential-shift-verlet or potential-switch)
dispcorr (EnerPres or no)
rcoulomb
rvdw
I read original papers about amber99fb,
Dear All,
I noticed that after my minimization run I have less snapshots in trr than
I expected.
For instance, the structure is written every 126-127 steps (plus the last
one)
even though my mdp file states
nstxout = 100
Best wishes,
Dawid Grabarek
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Gromacs Users mailing list
* Pleas
Dear Justin,
I was talking about changing GMXLIB, because she has to transfer her force
field files to a different directory than
Gromacs is installed in.
I am in the same situation and what I did was to copy a
whole gromacs-2016.4/share/top directory to my home
and changed GMXLIB for this direct
Hi,
You need to set the GMXLIB to directory with a modified forcefield. Just
copy all other files apart from aminoacids.rtp to a new directory with a
forcefield.
Also, if you want to be sure that you use a correct force field, you can
modify first line of forcefield.doc file into something like "M
constrain the
> configuration it is supplied, assuming that no constraints have yet been
> solved since it is a new run. If the coordinates supplied are from a
> previous simulation with constraints, then you are likely going to
> change them slightly, thus introducing a discontinuity
Dear All,
I start my MD simulation from a previous run using data in tpr and cpt
files
with changed mdp options for the new simulation.
Is it really important to use "continuation = yes" for the lincs
constraints.
What can be wrong if I don't (I use continuation = no).
Best wishes,
Dawid Grabarek
OK, I see. Thanks again!
pt., 2 sie 2019 o 17:07 Justin Lemkul napisał(a):
>
>
> On 8/2/19 8:59 AM, Dawid das wrote:
> > Thank you for an asnwer. However, I still need to ask more.
> > So, let's take this time the
> > NR1 CPH1 CPH2 H
> > NR1 CPH2 CPH1
ted in HSD. The
only reason I see is to
make it more rigid because I have "doubled" improper.
Best regards,
Dawid Grabarek
pt., 2 sie 2019 o 13:40 Justin Lemkul napisał(a):
>
>
> On 8/2/19 2:38 AM, Dawid das wrote:
> > Dear All,
> >
> > Why some of the improper
Dear All,
Why some of the improper parameters in CHARMM27 FF are repeated with
the middle atom types in a different order as in, e.g.
HR1 NR1 NR2 CPH22 0. 4.184
HR1 NR2 NR1 CPH22 0. 4.184
while some are not, e.g.
HR3 CPH1NR3 CPH1
Dear All,
I would like to make sure whether these parameters
O X X C 2 0. 1004.16
NH1 X X H 2 0. 167.36
under [ dihedraltypes ] card in ffbonded.itp file are the improper dihedral
parameters for the peptide bonds as defined in
Dear All,
I would like to make sure whether these parameters
O X X C 2 0. 1004.16
NH1 X X H 2 0. 167.36
under [ dihedraltypes ] card in ffbonded.itp file are the improper dihedral
parameters for the peptide bonds as defined in
Thank you.
niedz., 3 lut 2019 o 11:47 David van der Spoel
napisał(a):
> Den 2019-02-03 kl. 11:09, skrev Dawid das:
> > Dear Gromacs Users,
> >
> > I need to extract gro or pdb file with single snapshot from a trajectory
> > for a protein inside solvation box. In the o
Dear Gromacs Users,
I need to extract gro or pdb file with single snapshot from a trajectory
for a protein inside solvation box. In the output, I need whole protein
structure + all water molecules "inside" the protein. That could also mean
all water molecules within let's say 0.3 nm distance from
8-04-23 17:18 GMT+02:00 Justin Lemkul :
>
>
> On 4/23/18 11:15 AM, Dawid das wrote:
>
>> Dear All,
>>
>> Is it possible to create PDB file from XTC so that naming of histidine
>> residues
>> is HSE, HSD, HSP instead of HIS?
>>
>
> Yes, but only i
Dear All,
Is it possible to create PDB file from XTC so that naming of histidine
residues
is HSE, HSD, HSP instead of HIS?
Best wishes,
Dawid Grabarek
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can
The quick and dirty solution is that I write gro and g96 and copy
coordinates from the latter to the former, but I'd rather
have more elaborate solution.
2018-04-18 14:53 GMT+02:00 Dawid das :
> Dear All,
>
> I have similar issue. I have created xtc file with precision of 1.0e-6 n
Dear All,
I have similar issue. I have created xtc file with precision of 1.0e-6 nm
and I want my gro file to have the same precision,
and I get this at the end of trjconv
Reading frame 0 time3.000
Precision of npt-md-prod.xtc is 1e-06 (nm)
Setting output precision to 1e-06 (nm)
Last f
3.5 nm from the
side-chain carbon...
Sorry for bothering.
Best wishes,
Dawid
2018-04-15 16:41 GMT+02:00 Justin Lemkul :
>
>
> On 4/15/18 9:29 AM, Dawid das wrote:
>
>> Dear Gromacs Users,
>>
>> I run numerous MD simulations for similar systems of protein in water box
Dear Gromacs Users,
I run numerous MD simulations for similar systems of protein in water box
and
for only one system I encounter error:
*Fatal error:There is no domain decomposition for 4 ranks that is
compatible with the givenbox and a minimum cell size of 3.54253 nmChange
the number of ran
Dear Gromacs Users,
If I have some bonding parameters defined in aminoacids.rtp instead of
ffbonded.itp
I noticed that these parameters appear in my topology *top file.
If I change these parameters in *top file but not in aminoacids.rtp, and
get new *trp file with grompp will my parameters also c
OK, thank you.
2018-03-24 22:02 GMT+01:00 Mark Abraham :
> Hi,
>
> That coordinates will have three digits of precision, e.g from multiplying
> by 1000, truncating to an integer and dividing by 1000 again.
>
> Mark
>
> On Sat, Mar 24, 2018, 21:58 Dawid das wrote:
I checked again and it didn't.
2018-03-24 21:58 GMT+01:00 Mark Abraham :
> Hi,
>
> Did gmx rms warn you suitably that it was making guesses about masses?
>
> Mark
>
> On Sat, Mar 24, 2018, 21:07 Dawid das wrote:
>
> > Thank you Justin. In fact, editc
Dear Gromacs Users,
As in the topic. How do I understand default precision of 1000 for
*compressed-x-precision* option?
Best wishes,
Dawid Grabarek
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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't
definition and plausibly for
my new non-hydrogen atoms, the guessed mass
is that of carbon, while there are carbon, nitrogen, oxygen atoms.
Best regards,
Dawid
2018-03-24 20:56 GMT+01:00 Justin Lemkul :
>
>
> On 3/24/18 3:55 PM, Dawid das wrote:
>
>> Hi,
>> well actually
Hi,
well actually I used the same file to make minimize.tpr
Dawid
2018-03-24 20:51 GMT+01:00 Mark Abraham :
> Hi,
>
> That depends on what you used to make minimize.tpr. If it's different from
> the gro file then the rmsd will differ.
>
> Mark
>
> On Sat, Mar 24,
Dear Gromacs Users,
I get a bit different RMS when I use either minimize.tpr or
start-crystal-structure.gro as a reference structure.
This is definitely not because some atoms come across the
boundary as simulation progresses (I checked that). What could be
the reason? Does minimize.tpr use a diff
Dear Gromacs Users,
I have used 1000 kJ/(mol*nm^2) or 5000 kJ/(mol*nm^2) force constants
for restraining my protein atoms positions during steepest descent
minimization
and as I watch the "trajectory", the atoms of protein still change their
position.
The RMSD after 2000 steps is ca. 0.009 nm. Is
the restraint using
> plumed. Check the "Moving on a more complex path" in this tutorial (
> https://plumed.github.io/doc-v2.3/user-doc/html/belfast-5.html).
>
> Ruan
>
> On Mon, Mar 12, 2018 at 10:38 AM, Justin Lemkul wrote:
>
> >
> >
> > On
Dear Gromacs Users,
Is possible to decrease force constant for position restraints as the MD
simulation progresses? For instance I start with 1000 kJ/(mol *nm2) and
after 20 ps I go
to 800 kJ/(mol*nm2), then after 20 ps to 600 kJ/(mol*nm2), etc.?
Best wishes,
Dawid Grabarek
--
Gromacs Users mail
ogy, (ii) match it with the PDB file, and
> (iii) add an extra column at the end of the PDB with the respective
> charges. This should be relatively simple to do with your favorite
> scripting language.
>
> Cheers,
> J
>
> On Wed, Nov 8, 2017 at 11:12 AM, Dawid das wrote:
&g
Dear Gromacs Users,
I have a trajectory of my MD simulation in *.gro format. Is it possible to
write the pdb snapshot
from the trajectory so that the pdb file contains the atomic charge from
top file?
The charge should be put at the end of my pdb file.
Best wishes,
Dawid Grabarek
--
Gromacs User
Oh, I'm sorry for misleading you. You need use
-ter
The -noter means that you DON'T want to choose protonation yourself.
Give this one a try.
2017-08-06 20:38 GMT+02:00 ZHANG Cheng <272699...@qq.com>:
> Hi Dawid,
> Thank you. However, I still got three hydrogens after running:
>
>
> gmx pdb2gmx
Hi Cheng,
By default, the termini of a polypeptide are charged. You need option
-noter
in your gmx pdb2gmx command to interactively tell it what charge (no charge
in your case)
you want for your termini.
Best wishes,
Dawid
2017-08-06 20:20 GMT+02:00 ZHANG Cheng <272699...@qq.com>:
> Hi Mark,
>
Dear Gromacs Users,
I would like to get a simple plot of RMSD versus time for two trajectories
in *.gro
format, where RMSD is calculated between structures at the same time, i.e.
snap11 - snap12
snap21 - snap22
snap31 - snap32
snap41 - snap42
.
.
.
where snap31 means third snapshot of the first tr
in the sense of "between sensible atom indices" rather than
> suggesting that only one length is valid.
>
> Mark
>
> On Fri, 28 Jul 2017 14:41 Dawid das wrote:
>
> > Hi,
> >
> > No, those bonds I get the message were not constrained and virtually in
>
-07-28 13:33 GMT+02:00 Mark Abraham :
> Hi,
>
> It's hard to tell without seeing the messages and knowing whether those
> bonds were constrained.
>
> Mark
>
> On Fri, 28 Jul 2017 13:19 Dawid das wrote:
>
> > Dear Gromacs Users,
> >
> > I get a bun
Dear Gromacs Users,
I get a bunch of communicates when I run
gmx check -f npt-md2.xtc -s1 npt-md2.tpr >& gmx-check2.out
saying that I get different bond lengths than they should be. Can that be
caused by only 0.001 nm precision of my results?
Also I am not exactly sure if I understand correctly w
By the way, why does this vector change during simulation? What if I use
>> exactly the same vector for my whole
>> simulation?
>>
>>
> This is the function of pressure coupling. If you keep the box vectors
> fixed, that is an NVT simulation.
Aaaah, very well then. Thank you for explaining that
>
> On 6/5/17 10:07 AM, Dawid das wrote:
>
>> Dear Gromacs Users,
>>
>> Suppose I have a trajectory file in gro format. If I change the last line
>> for each
>> snapshot (i.e. line with box vectors values) into an arbitrary set of
>> three
>> numb
Dear Gromacs Users,
Suppose I have a trajectory file in gro format. If I change the last line
for each
snapshot (i.e. line with box vectors values) into an arbitrary set of three
numbers,
will it have impact on further manipulations of this gro trajectory file
with trjconv?
In other words, is the
what extent do I violate the applicability of parameters that were
optimized based on a different algorithm?
Dawid
2017-05-21 0:30 GMT+02:00 Justin Lemkul :
>
>
> On 5/20/17 8:28 AM, Dawid das wrote:
>
>> Hi Mark,
>>
>> Thank you. Actually I want to do some QM/MM
Hi Jane,
I don't know if you can do that with one of Gromacs tools, but you can
easily extract your bond length/angle values
as a function of time with gmx distance and gmx angle, respectively.
Then, knowing the formula for bond and angle energies as well as parameters
(force constants and referenc
> Mark
>
> On Fri, 19 May 2017 18:44 Dawid das wrote:
>
> > Dear Gromacs Users,
> >
> > I am a bit confused whether I shouldn't use charge
> > group-based cut-off for electrostatics when using CHARMM22.
> > If I shouldn't use it, what is
Dear Gromacs Users,
I am a bit confused whether I shouldn't use charge
group-based cut-off for electrostatics when using CHARMM22.
If I shouldn't use it, what is the purpose of specification of charge
groups in
original CHARMM files?
Best wishes,
Dawid
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Gromacs Users mailing list
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Dear Gromacs Users,
I would like to hear your advice on scaling 1,4-interactions for both
classical and
QM/MM molecular dynamics simulations. I am using CHARMM27 force field.
Firstly, for classical MD, according to this post
https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=10
Yes, you are right. This is due to limited precision of xtc file. For trr I
don't get the same.
I would never expect such large discrepancies. Thank you very much!
2017-05-06 16:33 GMT+02:00 Jochen Hub :
>
>
> Am 06.05.17 um 15:35 schrieb Dawid das:
>
>> Dear Gromacs
Dear Gromacs Users,
I am a bit anxious about the results I get for my simulation of protein in
a box of water using CHARMM 27 force field.
Namely, even though I use following options to constrain bond lengths
between
hydrogen atoms and heavy atoms:
constraint_algorithm= lincs
constraints
Hello Dilip,
I don't really get what your problem is. What do you actually want to do?
Read-in and parse a *.gro file which
is output from MD simulation? Then for instance, your Python script should
calculate something from, e.g. distance
between centres of masses of residues of interest?
Or do y
Hi,
I guess you can try
gmx trjconv -f file.gro -o file.pdb -pbc mol -s file.tpr -center
2017-01-18 16:14 GMT+01:00 Irem Altan :
> Hi,
>
> I have a trajectory saved in .gro format. It has multiple frames/snapshots
> in it. I’m using .gro format because I needed higher precision than
> standard
Since I join this discussion, this is perhaps a good moment to ask
following questions.
I use Gromacs 5.0.4 and the file.mdp options that I found here
http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM , so:
1. The bug that was described here
https://github.com/NMRLipids/NmrLipid
Also, you could try to find something in these articles:
http://apps.webofknowledge.com/Search.do?product=WOS&SID=P2QP4ybhv2TW78yMOMx&search_mode=GeneralSearch&prID=9bcb8bea-c281-4524-a7de-e664898a322b
2017-01-11 13:48 GMT+01:00 Dawid das :
> You might also want to read the Defau
You might also want to read the Default section over here:
http://charmm.sunhwanj.com/html/nbonds.html
where following ''equations'' give you correspondence between CHARMM and
Gromacs keywords
rvdw-switch == ctonnb, rlist == cutnb, rvdw == ctofnb
2017-01-11 13:36 GMT+01:
Hi,
I believe that Mohsen here did not ask about what you are writing about
Mark. He asks about cut-offs not the exponents
in the LJ formula.
I am no expert in that but I reviewed Andrew Leach's book on that and also
other resources and I did not find
any reason why lower and upper cut-off for LJ
Thank you, now I understand relationship between beta and ewald_rtol :).
I will read the article you suggested and let you know if I have further
questions.
2017-01-02 19:00 GMT+01:00 Mark Abraham :
> Hi,
>
> On Mon, Jan 2, 2017 at 6:31 PM Dawid das wrote:
>
> > I went t
I went through this manual before posting these questions, and I'm sorry if
I'm to blind to see that but
I don't understand how they would answer my questions. Could you give me a
clearer explanation, please?
Dawid
2017-01-02 18:19 GMT+01:00 Mark Abraham :
> On Mon, Jan 2, 201
Dear All,
I have at least two questions regarding PME in Gromacs 5.0.4.
Firstly, in my *.log file there is a line that reads
Will do ordinary reciprocal space Ewald sum.
Using a Gaussian width (1/beta) of 0.384195 nm for Ewald
Is "beta" the relative weight of direct and reciprocal sums? If this
Thank you! I will definitely have a close look at that.
Best regards,
Dawid
2016-12-19 2:33 GMT+01:00 Justin Lemkul :
>
>
> On 12/18/16 12:22 PM, Dawid das wrote:
>
>> Dear All,
>>
>> Have you ever seen a script/tool that allows for transformation of the
>&g
Dear All,
Have you ever seen a script/tool that allows for transformation of the
Gromacs force field files
into CHARMM force field files? I can see that there is a Pythons script
that does the other
way around.
Also I could use a tool that creates *.psf file from *.top file. I googled
for that an
Dear Gromacs Experts,
I have created two RMSD plots of my protein. For one, as a reference
structure source,
I have used file.gro and in the other a file.tpr, both from previous
calculations. I have obtained
slightly different values and i.e. plots. Is that because my reference
structures where di
nge their atom names?
>
> Dading Huang
>
> On Wed, Nov 9, 2016 at 7:23 PM, Dawid das wrote:
>
> > Dear Gromacs Experts,
> >
> > I know how to specify which Glu/Asp residues are to be
> > protonated/deprotonated with
> > pdb2gmx tool. However, I do not l
Dear Gromacs Experts,
I know how to specify which Glu/Asp residues are to be
protonated/deprotonated with
pdb2gmx tool. However, I do not like that the hydrogen is added to one of
the oxygen atoms
of carboxyl moiety. I would like it to be found on the other oxygen. Is
there any other way
except mo
O'right, I found my mistake.
Now it works fine.
Thank you!
2016-03-09 16:11 GMT+01:00 Justin Lemkul :
>
>
> On 3/9/16 10:11 AM, Dawid das wrote:
>
>> 2016-03-09 16:07 GMT+01:00 Justin Lemkul :
>>
>>
>>> You are. That's what -all is for:
>>
2016-03-09 16:07 GMT+01:00 Justin Lemkul :
>
> You are. That's what -all is for:
>
> "Plot all angles separately in the averages file, in the order of
> appearance in the index file."
>
> Open up angaver.xvg and you will see the average, then the two individual
> time series.
Than something do
Dear Gromacs Experts,
How can I get a plot of a bond length/ valence angle/ dihedral angle during
simulation
from *xtc and *.ndx files? I am pretty sure that it is possible, but with
g_angle
and g_bond I can get only the distribution.
By the way, when I use
g_angle -f npt-md2-cent.xtc -n index.nd
Very well. Thank you!
2016-03-06 17:25 GMT+01:00 Justin Lemkul :
>
>
> On 3/6/16 11:17 AM, Dawid das wrote:
>
>> Dear Gromacs Experts,
>>
>> Why for some atomtypes the charges are different in ffnonbonded.itp and
>> aminoacids.rtp files?
>> For instanc
Dear Gromacs Experts,
Why for some atomtypes the charges are different in ffnonbonded.itp and
aminoacids.rtp files?
For instance
for CD1 CA 0.035 8
from TRP residue the charge for CA type residue is actually -0.115
Does it mean that van der Waals parameters for this CD1 atom of
Yes of course, but I have already performed a few of simulations. Too bad.
I need to repeat them.
However, final question. Other atom names can start with M?
DG
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Oh gosh..., so in that case is there any other way around to constraint
those MH11 - MCB1 etc. bond lengths except for renaming all hydrogen atoms?
Best wishes,
Dawid Grabarek
2016-03-01 19:29 GMT+01:00 Justin Lemkul :
>
>
> On 3/1/16 1:24 PM, Dawid das wrote:
>
>> Dear Gromac
Dear Gromacs Experts,
I am pretty sure I have already answered this question long time ago but I
cannot find
it. What I did is I added a new residue for my system and it contains
hydrogen atoms.
Now, the thing is that all atoms names start with "M", so I have MH21,
MH22, MCA1, etc.
atoms. I want t
Dear Gromacs Experts,
I run gmx pdb2gmx and it runs without any warnings or errors by the *.top
file does not
contain any bonds. The *.gro file is fine and all hydrogen atoms are added
correctly.
Now I have discovered that when I get rid of calcium ions in my *.pdb file
I get proper
*.top file. B
2016-02-27 22:42 GMT+01:00 Justin Lemkul :
> Content is read by position, which is precisely your problem.
>
Yes, I am aware of that. By I did not change anything in position of my
*.pdb file.
I know that in different years the format changes somehow. The *.pdb file I
am using is from 1998.
The
Dear Gromacs Experts,
I have created a new residue for which atom names in my *.pdb file are
4-signs long.
When I run gmx pdb2gmx I get following error
Fatal error:
Atom MCA in residue CH6 65 was not found in rtp entry CH6 with 33 atoms
while sorting atoms.
I am absolutely one hundred percent su
your original.gro using editconf and in the final
> gro file will be corrected.
>
> On Wed, Feb 3, 2016 at 11:24 AM Dawid das wrote:
>
> > So it turns out that what is important is the order, i.e. when I want
> > connection
> > between residues 164 and 165 they need to
>
> Atom numbering is unimportant, but you might see warnings from tools that
> recognise it is weird. Residue numbering is important only in that the
> value changes when the residue does - it doesn't have to go up by one. Try
> it and see ;-)
>
> Mark
>
> On Wed, 3 Feb
Dear Gromacs Experts,
Let's assume that I have a *.gro file in a proper format but the number of
atoms and/or
residues is let's say random, e.g. I have coordinates of atoms for residue
87, 95, 96, 88.
What is more, I have let's say 76 atoms in the system, but I start
numbering from 999.
Will I be
Generally one would use acetyl or N-methylamine capping groups respectively
> for N and C termini of cleaved peptide bonds. These are often called ACE
> and NME in .rtp files.
>
> Mark
>
> On Tue, Feb 2, 2016 at 2:58 PM Dawid das wrote:
>
> > Dear Gromacs Experts,
>
Dear Gromacs Experts,
I would like to perform MD simulation of a system consisting of few amino
acids
cut out of the protein. The thing is that I break some peptide bonds and I
add methyl
groups in this place. Now I am missing charmm22 parameters for proper bonds.
Could you give me a tip on gettin
Thank you.
2015-09-17 12:37 GMT+01:00 Mark Abraham :
> Hi,
>
> Yes. Further options at
> http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
>
> Mark
>
> On Thu, Sep 17, 2015 at 1:04 PM Dawid das wrote:
>
> > O'right, I have figured th
O'right, I have figured that out myself. Just use text file like data.txt
with two lines:
1
1
and redirect it: g_rms [options] < data.txt
2015-09-17 11:32 GMT+01:00 Dawid das :
> Dear Gromacs Experts,
>
> Let's say that for some reasons I don't want to specify the
Dear Gromacs Experts,
Let's say that for some reasons I don't want to specify the atom group when
g_rms (or other module) prompts me to do so.
So I do not want to see this:
Select group for RMSD calculation
Group 0 ( System) has 38387 elements
Group 1 (Protein) has 3470 e
trajectory in parallel, using separate g_rms processes, then concatenating
>> the output. Use -b and -e options to limit the analysis to specific
>> intervals.
>>
>> Kind regards,
>> Erik
>>
>> On 15 Sep 2015, at 13:37, Dawid das wrote:
>>>
>>
Erik's strategy if you break the trajectory into
> parts with trjconv, convert it to .xtc, or write it as .xtc in the first
> place. See also
>
> http://www.gromacs.org/Documentation/How-tos/Reducing_Trajectory_Storage_Volume
>
> Mark
>
> On Tue, Sep 15, 2015 at 2:59 P
hat what I should expect?
2015-09-15 13:45 GMT+01:00 Dawid das :
> Dear All,
>
> Thank you all. Especially for your tip Erik ;).
>
> Dawid
>
> 2015-09-15 13:42 GMT+01:00 Erik Marklund :
>
>> Dear Dawid,
>>
>> The best thing I can think of is to analyse dif
put. Use -b and -e options to limit the analysis to specific
> intervals.
>
> Kind regards,
> Erik
>
> > On 15 Sep 2015, at 13:37, Dawid das wrote:
> >
> > Dear Gromacs Experts,
> >
> > I have an enormous *trr file, which has 1 000 000 points. Now, I kn
Dear Gromacs Experts,
I have an enormous *trr file, which has 1 000 000 points. Now, I know that
I can modify this file with trjconv, but let's say I do not want to do it,
but I want to have my 1 000 000 points in *xvg file when I use g_rms for
instance.
Is there a way to accelarate it?
Best wish
Dear Atila,
I am no specialist but in general all force fields are designed to recover
specific properties.
So that other can give you more tips, tell us what your aim is. Why do you
want to simulate RNA
and what properties or phenomena are you interested in?
Best wishes,
Dawid Grabarek
2015-09
O'right, it seems that I did everything correctly.
Thank you for your help! :)
2015-09-05 14:30 GMT+01:00 Dawid das :
> Yes, that is right Justin. But I still need:
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = Protein non-P
Justin Lemkul :
>
>
> On 9/5/15 5:48 AM, Dawid das wrote:
>
>> I struggle to properly define my *mdp file. I have following keywords and
>> their values:
>>
>> ;Simulated annealing is on
>> annealing = single
>> annealing-npoints = 30 30
&
, grompp says:
Fatal error:
Not enough annealing values: 1 (for 2 groups)
I believe I do everything according to the documentation.
2015-09-04 22:41 GMT+01:00 Dawid das :
>
> 2015-09-04 22:03 GMT+01:00 Vitaly V. Chaban :
>
>> However, your simulation schedule makes little s
2015-09-04 22:03 GMT+01:00 Vitaly V. Chaban :
> However, your simulation schedule makes little sense physically .
>
What do you mean by that? I just want to heat up my system gently before
equilibration phase.
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Dear Gromacs Experts,
Is it possible to do following heating of my system:
increase reference temperature by 20 K every 5 ps of simulation in one run
until I reach 300 K?
According to what I found in one of papers, it is possible to do with NAMD.
Best wishes,
Dawid Grabarek
--
Gromacs Users ma
It seems to work :). Thank you!
2015-09-04 9:52 GMT+01:00 Dawid das :
>
> 2015-09-03 13:06 GMT+01:00 Justin Lemkul :
>
>> FYI, CHARMM22 has no CMAP. CHARMM22/CMAP (what GROMACS somewhat
>> misleadingly calls "charmm27.ff") does.
>>
> Yes, I was aware of
2015-09-03 13:06 GMT+01:00 Justin Lemkul :
> FYI, CHARMM22 has no CMAP. CHARMM22/CMAP (what GROMACS somewhat
> misleadingly calls "charmm27.ff") does.
>
Yes, I was aware of that, just forgot to write CHARM22/CMAP.
>
> My question is, whether there is a way to use CMAP parameters only for
>> con
Dear Gromacs Experts,
I am working with fluorescent protein, posesing a chromophore which I
defined as a non-standard " amino-acid residue". Now, I want to use
Charmm22 force field and the issue is that I am missing CMAP parameters and
these are not available in the literature.
My question is, wh
Dear Gromacs Experts,
I am pretty surprised with following finding. When I rerun my simulation
and want to append energy, trajectory, etc. to previous files, appending
works if and only if I do not change the directory where I rerun
calculations.
For instance there is dir1 where I run MD1. Then I
Dear Gromacs experts,
Although I have read both online and printed Gromacs manual I am still not
sure how the error estimate value is calculated when I use g_energy and
choose pressure or density for instance.
Could you explain it in simple words?
Best wishes,
Dawid Grabarek
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Gromacs Users m
> > > You've *tried* to use flexible water. But does your water itp file
> > *have* a
> > > flexible implementation that your approach will trigger?
> > >
> > > Mark
> > >
> > > On Sun, 9 Aug 2015 19:42 Dawid das wrote:
proach will trigger?
>
> Mark
>
> On Sun, 9 Aug 2015 19:42 Dawid das wrote:
>
> > 2015-08-09 18:27 GMT+01:00 Mark Abraham :
> >
> > >
> > > Justin's advice is true only if your water topology has a flexible
> > > implementation. Check it
>
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