Hi Chris
My EM works just fine if I use a cubical box of water, so I'm baffled as
to what's going wrong in this case.
I tried the entire process again, this time removing position restraints.
Let me describe my entire procedure on this occasion, once again:
1) I first assembled a bilayer of 128
Dear Arman,
I've noticed a similar effect where large voids appear in a solvent when
running long nose-hoover NVT simulations. I have checked and it is not a pbc
artefact.
I found that if I turn the thermostat off the holes go away. I've also found
that reducing the number of cores removes the hol
Dear Richard,
Thank you for your kind response. I'm glad that my problem is not a rare
one. Actually, I apply the simplest V-rescale as the thermostat. I run my
system on one core! However, I have not tried turning off the thermostat
and run a micro-canonical instead.
Well, I got an idea to implem
Dear Gmx Users,
I made a biphasic system with water and hexane following Justin tutorial (800
hexane molecules) ,after adding the peptides in water phase, the number of the
hexane molecules were reduced and some of them were shifted to the other
side of water molecules (not at the interface of
On 10/30/12 3:28 AM, Bharath K. Srikanth wrote:
Hi Chris
My EM works just fine if I use a cubical box of water, so I'm baffled as
to what's going wrong in this case.
I tried the entire process again, this time removing position restraints.
Let me describe my entire procedure on this occasion,
On 10/30/12 5:21 AM, Davoud Zare wrote:
Dear Gmx Users,
I made a biphasic system with water and hexane following Justin tutorial (800
hexane molecules) ,after adding the peptides in water phase, the number of the
hexane molecules were reduced and some of them were shifted to the other side
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
You show different atoms before and after minimization so this is not proof of
movement.
I often resize my box by changing the value at the end of the file and have
never had any problem with it. Of
course, you do need to be careful with this and everything you do.
Chris.
-- original message
Hello, everyone!
I'm a new user in gromacs, and now I have to perform a steered pulling code
on a ligand-receptor complex. The ligand is to be pulled away from the binding
site of the receptor, and umbrella sampling will be used to gain the PMF
(potential mean force) curve. Then binding en
Dear Arman,
I have never seen holes appear in my solvent when running on 12 cores or
fewer, or when running with langevin coupling or NVE.
Running at higher temperatures (700K-1000K) did remove the holes from my
system however, the RDF's were inconsistent on varying core counts
(peeks and tr
That seemed to fix it. Thank you so much!
Regards
Bharath
>Do not manually resize the box. Use editconf -box and -center as
>appropriate to
>place all your components within the unit cell. While it may appear from
>visualization that your molecules are where you want them to be, they are
>not.
Hi Gmxers,
has anyone ever converted the GROMACS hessian (in ps^(-2)) to CHARMM hessian
(in KCal/mol),
even considering the individual unit, GROMACS hessian numbers are far bigger
than those in CHARMM?
thanks,
Yao
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When trying to do an npt run, I get the fatal error: The X-size of the box
(3.999511) times the triclinic skew factor (1.00) is smaller than the
number of DD cells (4) times the smallest allowed cell size (1.00). I
should mention, I'm brand new to using gromacs so any assistance is greatly
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