I got it to work finally. Didn't install fftw earlier. Thanks.
On Fri, Mar 5, 2010 at 4:02 PM, Mark Abraham wrote:
> On 6/03/2010 5:05 AM, Dian Jiao wrote:
>
>> Actually, I tried 4.0.7 first from this link,
>> http://www.gromacs.org/index.php?title=Download_%26_Installation
>>
>> It didn't work (
On 6/03/2010 1:19 AM, Carla Jamous wrote:
Hi,
please I'm having a problem while running a minimisation.
I prepared my system with pdb2gmx and generated .pdb files. From the
last pdb file, I did grompp & generated the tpr file that I used to
start my minimization. At the 46th step, I encountered
On 6/03/2010 5:05 AM, Dian Jiao wrote:
Actually, I tried 4.0.7 first from this link,
http://www.gromacs.org/index.php?title=Download_%26_Installation
It didn't work (same error). That's why I downloaded 4.0.6 from the same
webpage.
On Fri, Mar 5, 2010 at 10:51 AM, Justin A. Lemkul mailto:jalem.
I am using SPC/E water model. Regarding isopropanol, these are the partial
charges:
"H1"0.038594
"C1"0.147250
"HC1" 0.038591
"C2"-0.106023
"HC2" 0.038591
"HC3" 0.038591
"HA1" 0.038591
"C3"-0.106023
"HA2" 0.038591
"HA3" 0.038591
"O1"-0.579340
"HO1" 0.373996
A
Hi,
i observed the following problem. if i simulate water (spc or tip4p)
with gromacs 4.0.5 i get with v-rescale or berendsen thermostat the
wrong temperature (ref_t = 300K -> average around 425K, in about 1-2ps),
but only in serial, not in parallel runs.
non-water molecules or nose-hoover the
On 2010-03-05 20.51, Jose Borreguero wrote:
Dear GROMACS users,
I am simulating aqueous isopropanol. Unfortunately I observe segregation
of isopropanol from SPC water at isopropanol fraction volume of 0.25.
Since isopropanol is miscible in water, my parameters stress too much
the hydrophobic cha
Dear GROMACS users,
I am simulating aqueous isopropanol. Unfortunately I observe segregation of
isopropanol from SPC water at isopropanol fraction volume of 0.25. Since
isopropanol is miscible in water, my parameters stress too much the
hydrophobic character of this solute. Only a few interstitial
Dian Jiao wrote:
Actually, I tried 4.0.7 first from this link,
http://www.gromacs.org/index.php?title=Download_%26_Installation
It didn't work (same error). That's why I downloaded 4.0.6 from the same
webpage.
Well, downgrading is usually not the answer, especially if you're downgrading t
Actually, I tried 4.0.7 first from this link,
http://www.gromacs.org/index.php?title=Download_%26_Installation
It didn't work (same error). That's why I downloaded 4.0.6 from the same
webpage.
On Fri, Mar 5, 2010 at 10:51 AM, Justin A. Lemkul wrote:
>
>
> Dian Jiao wrote:
>
>> I was following t
Dian Jiao wrote:
I was following the instruction to install gromacs 4.0.6 on my machine.
./configure --enable-threads --enable-float --|enable-sse --prefix=[mypath]|
make
make install
The configure looks ok but no Makefile is generated. When I do make or
make install, it gives me the error:
I was following the instruction to install gromacs 4.0.6 on my machine.
./configure --enable-threads --enable-float --enable-sse --prefix=[mypath]
make
make install
The configure looks ok but no Makefile is generated. When I do make or make
install, it gives me the error:
make: *** No targets sp
tekle...@ualberta.ca wrote:
Hi Justin,
That is really confusing. I tried to run this PDB file many times. But
still I could not get it the topology file. I waited for so long (10
hrs)but still the code looks in a deadlock.
Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat
S
Hi Justin,
That is really confusing. I tried to run this PDB file many times. But
still I could not get it the topology file. I waited for so long (10
hrs)but still the code looks in a deadlock.
Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat
Select the Force Field:
0: GR
Hi all,
to summerize the
seems really like a compiler problem. i have now compiled 4.0.5 with gcc
and had no problems.
i don't really know which icc compiler it was (but had send the guy who
installed gromacs a mail), but with 'which icc' i find:
/share/apps/intel/cce/9.1.046/bin/icc
i will t
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I don't think the atom number is the problem. I also have systems with more
than 9 atoms, and in the gro file the atom number after 9 is reset
to 0, but that was never a problem for the simulations. I would check the
parameters again, but I don't have a more exact answer to your problem.
2
Hi,
please I'm having a problem while running a minimisation.
I prepared my system with pdb2gmx and generated .pdb files. From the last
pdb file, I did grompp & generated the tpr file that I used to start my
minimization. At the 46th step, I encountered the problem:"water molecule
cannot be settle
Hi,
Can you also post your .mdp?
Ran
Berk Hess wrote:
> Hi,
>
> I have never heard about problems like this before.
> It seems highly unlikely to me that the innerloops are causing this.
>
> Are your running exacly the same tpr file on your local machine
> and the cluster?
>
> You probably want
Hi,
I have never heard about problems like this before.
It seems highly unlikely to me that the innerloops are causing this.
Are your running exacly the same tpr file on your local machine
and the cluster?
You probably want to update to version 4.0.7 to be sure you have
all the latest bugfixes.
Hi,
i have the following problem: (GROMACS 4.0.5)
when i simulated water in serial on our cluster with the brendsen or
v-rescale thermostat i get to high temperatures (300 K goes in very
short time up to around 425 K). If i simulate in parallel or at my local
machine i get no problems. Also if
> Respected experts
> I want to calculate the self diffusion cofficient of an oxygen molecule in
> water. The experimental value in the literature is found to be 2.5 x 10-9
> nm2/s at 1atm pressure (density 997) and 25. I have considered cut-off
> Lennard Jones interaction between water and oxyg
Hi,
You don't want to mess with the topology, you will be simulating a quit
different
system when you turn off constraints. Also Gromacs does not optimize based
on names, since the name might not say anything about the molecule.
I don't know what effect of what optimizations you want to test,
bu
Dear all,
I simulated water (spc) with the ffG53a5 force field. For testing
propose i want to turn of the water optimisation. How do i do this?
So far i have tried:
* contraints = none
* define = -DFLEXIBLE
* took the spc.itp file and deleted all the stuff for settle and the
other force fields,
Hi,
If i remember correctly SPC/E water might be worth trying. There is plenty
of research paper in this field. Try this paper
http://pubs.acs.org/doi/abs/10.1021/jp003020w
Also P,T coupling have effects on Diffusion Coeff.
amit
On Fri, Mar 5, 2010 at 1:29 AM, Sunil Thapa wrote:
> Respected
Sunil Thapa skrev:
Respected experts
I want to calculate the self diffusion cofficient of an oxygen
molecule in water. The experimental value in the literature is found
to be 2.5 x 10-9 nm2/s at 1atm pressure (density 997) and 25. I have
considered cut-off Lennard Jones interaction between wat
Respected experts
I want to calculate the self diffusion cofficient of an oxygen molecule in
water. The experimental value in the literature is found to be 2.5 x 10-9 nm2/s
at 1atm pressure (density 997) and 25. I have considered cut-off Lennard Jones
interaction between water and oxygen. I want
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