Dear Justin,
I have been practicing umbrella sampling simulations following your tutorial
step by step. I have just finished to perform the pull simulations to
identify the configurations to use in the umbrella runs. I have used the
distances.pl script to run iteratively g_dist and the resulting f
Dear Gromacs users,
Is a vacuum md simulation an NVT simulaton? As the pressure and energy are
not fixed, I think that the only option left is NVT. But without pbc, the
volume would not have been defined. Can it still be called NVT?
Thanks,
Jong Wha
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gmx-users mailing listgmx-us
Hi,
Visualization is the key. If you check the structure right after genbox,
you should be able to notice something odd. Apparently genbox has a problem
with martini water, which probably means there is a problem with monoatomic
solvents. The problem has been noted before, b ut I'm a bit too lazy
The check point file you submit will have the velocity information.
On Tue, Dec 11, 2012 at 10:55 AM, Bahar Mehrpuyan
wrote:
> hi gmx user
>
> I've done a production simulation with gen_vel= no, but in grompp I forgot
> that use .trr file of equlibration simulation for initial velocities,
> my q
hi gmx user
I've done a production simulation with gen_vel= no, but in grompp I forgot that
use .trr file of equlibration simulation for initial velocities,
my question is how gromacs treats with initial velocities in this case?
thanks in advance.
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gmx-users mailing listgmx-users@gromacs
On Mon, Dec 10, 2012 at 11:54 PM, Justin Lemkul wrote:
>
>
> On 12/10/12 5:45 PM, francesco oteri wrote:
>
>> For Justin,
>> I need this water for one simple reason: less then 20nm doesn't workAs
>> I said before
>>
>>
> It seems you have identified the source of the problem, and it is
> inde
On Mon, Dec 10, 2012 at 11:44 PM, francesco oteri wrote:
> Hi Mark,
> you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to
> use 0.21. Since I still got errors with this procedure, I decided to remove
> water manually through vmd.
>
Don't change things until you know *why* t
On 12/10/12 5:45 PM, francesco oteri wrote:
For Justin,
I need this water for one simple reason: less then 20nm doesn't workAs
I said before
It seems you have identified the source of the problem, and it is independent of
box size. I questioned the box size because it seemed rather ran
For Justin,
I need this water for one simple reason: less then 20nm doesn't workAs
I said before
2012/12/10 francesco oteri
> Hi Mark,
> you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to
> use 0.21. Since I still got errors with this procedure, I decided to remove
>
Hi Mark,
you are right respect the -vdwd 0.4: In MARTINI tutorials they suggest to
use 0.21. Since I still got errors with this procedure, I decided to remove
water manually through vmd.
Looking carefully at the configurations, I found that the water molecule
originating the error is exactly super
On Mon, Dec 10, 2012 at 11:15 PM, francesco oteri wrote:
> Actually, since I copied and pasted the mail, there is an imprecision. When
> I use 20nm as box side lenght I don't get
> any error, everything goes fine.
>
> I actually tested different size between 19 and 20 nm and I found that the
> mi
On 12/10/12 5:15 PM, francesco oteri wrote:
Actually, since I copied and pasted the mail, there is an imprecision. When
I use 20nm as box side lenght I don't get
any error, everything goes fine.
I actually tested different size between 19 and 20 nm and I found that the
minimum size to avoid th
Actually, since I copied and pasted the mail, there is an imprecision. When
I use 20nm as box side lenght I don't get
any error, everything goes fine.
I actually tested different size between 19 and 20 nm and I found that the
minimum size to avoid the error is 19.5nm.
My system has an average size
On Mon, Dec 10, 2012 at 9:48 PM, francesco oteri
wrote:
> Dear gromacs users,
>
> I am facing a very tricky problem in building a stable topology.
> In particular I am trying to use MARTINI force-field and I noticed that if
> I use a box whose the side size is smaller than 20nm, the minimization
>
On 12/10/12 3:48 PM, francesco oteri wrote:
Dear gromacs users,
I am facing a very tricky problem in building a stable topology.
In particular I am trying to use MARTINI force-field and I noticed that if
I use a box whose the side size is smaller than 20nm, the minimization
fails with this mes
On 12/10/12 3:13 PM, Andrew DeYoung wrote:
Javier and Mark,
Thank you SO much! That is so helpful to me.
If you have time, I have two follow-up questions:
(1) From your answer, it seems that in OPLS, 1-4 interactions will be taken
into account (scaled by fudge) ONLY if the 1-4 atomic indice
On 12/10/12 3:27 PM, Andrew DeYoung wrote:
Hi again,
I forgot to mention that in my system I always set nrexcl = 3 (while
explicitly specifying 1-4 interactions in [ pairs ], as I mentioned in my
last message). Does this mean that if gen-pairs = yes, then 1-5, 1-6, 1-7,
..., 1-Infinity nonbon
Hi again,
I forgot to mention that in my system I always set nrexcl = 3 (while
explicitly specifying 1-4 interactions in [ pairs ], as I mentioned in my
last message). Does this mean that if gen-pairs = yes, then 1-5, 1-6, 1-7,
..., 1-Infinity nonbonded interactions will automatically be taken i
Javier and Mark,
Thank you SO much! That is so helpful to me.
If you have time, I have two follow-up questions:
(1) From your answer, it seems that in OPLS, 1-4 interactions will be taken
into account (scaled by fudge) ONLY if the 1-4 atomic indices are specified
in [ pairs ], even if gen-pairs
On 12/10/12 10:50 AM, Steven Neumann wrote:
Would you also specify in each US window specific residue instead of
the whole protein?
That really depends on whether the residue-ion distance reflects the desired
reaction coordinate and if doing so is superior to using the protein-ion
distance
Would you also specify in each US window specific residue instead of
the whole protein?
Sreven
On Mon, Dec 10, 2012 at 2:47 PM, Steven Neumann wrote:
> On Mon, Dec 10, 2012 at 2:11 PM, Justin Lemkul wrote:
>>
>>
>> On 12/10/12 9:01 AM, Steven Neumann wrote:
>>>
>>> Dear Gmx Users,
>>>
>>> I am
On Mon, Dec 10, 2012 at 2:11 PM, Justin Lemkul wrote:
>
>
> On 12/10/12 9:01 AM, Steven Neumann wrote:
>>
>> Dear Gmx Users,
>>
>> I am pulling away cation from the protein glutamic acid residue with:
>>
>> pull= umbrella
>> pull_geometry = distance ; simple distance increase
>> pul
On 12/10/12 5:18 AM, Anders Lervik wrote:
Dear all,
I have been simulating an inhomogeneous system consisting of a membrane and
a solvent (e.g a lipid bilayer solvated in water). In these simulations, I
have noticed lateral movement in the COMs of the membrane and solvent -
they move in opposi
On 12/10/12 9:01 AM, Steven Neumann wrote:
Dear Gmx Users,
I am pulling away cation from the protein glutamic acid residue with:
pull= umbrella
pull_geometry = distance ; simple distance increase
pull_dim= N N Y
pull_start = yes ; define initial COM distance
Also, building yourself a test system of (for example) a single amino acid,
varying the .top settings, compiling a .tpr and using mdrun -rerun to
investigate the effects can be a good way to acquire confidence that the
physics you are implementing does match the model you intend.
Mark
On Mon, Dec
On Sunday, December 9, 2012 at 7:48 PM SeokYun123 wrote:
>I'm trying to download topolbuild1_2_1 in my Mac computer.
First, why are you using 1.2.1 instead of 1.3 which is also available in the
user
contributed software section at gromacs.org? Actually, there should be a
topolbuild1_3_1 cont
Hi Andrew!
In addition to Justin's reply, I would like to point out that this is
something you can easily answer yourself by building a few atoms
system using your .itp file and running gmxdump to look at the actual
values stored in the .tpr.
Cheers,
Bogdan
On Sat, Dec 8, 2012 at 6:53 PM, Andrew
Indeed, thanks Javier.
These kinds of features are a bit awkward to document because there are
lots of conditions under which various forms of interaction generation are
used - primarily varying with the forcefield. Different force fields
motivate various capabilities of pdb2gmx and it's not fully
Dear all,
I have been simulating an inhomogeneous system consisting of a membrane and
a solvent (e.g a lipid bilayer solvated in water). In these simulations, I
have noticed lateral movement in the COMs of the membrane and solvent -
they move in opposite directions such that the overall center of
Hi
The pair section specifies the atoms between which a non-bonded
interaction will be build up, even if the "normal" non-bonded is
excluded, what is a mechanism to build 1-4 interactions. So, if you want
a 1-4 interaction to be taken into account, you need to specify it in
the topology, in t
Correct, C1060 does not have the CUDA 2.0 compute capability required for
GROMACS 4.6. We will not have the ability to support GPU cards of lower
capability in the future. Unfortunately, your only GROMACS options are
probably to use the OpenMM functionality in 4.5.x (which is still present
in 4.6,
Hard to say. Your compiler is prehistoric, and things to do with pthreads
are the province of the compiler, so getting a more recent version will
probably fix it.
Mark
On Mon, Dec 10, 2012 at 7:32 AM, BHARATI DUTTA wrote:
> Hi,
>
> The following error pops up during compilation of Gromacs-4.5.5
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