Hello:
I am trying to do umbrella sampling for a protein/ligand water system
these days following Justin's nice tutorial. And I've got some questions:
(1) in the tutorial, the small peptide was pulling along Z direction. I
am just wondering, will the small peptide be pulled in both +Z and -Z
Dear gmx,
I understood that CHARMM supports two neutral/protonated histidine (HSD/HSE)
and fully protonated(HSP). How about the heme bound HIS version? I couldn't
find the HIS1 which knows as histidine bound to a heme? how do i link the heme
bound his using charmm27.ff.
--
gmx-users mailing
Thank you Mark and Francesco. I will be pleased to contribute with a fix in
case I come up with a fairly general solution for this issue.
Best regards,
João Henriques
On Thu, Apr 4, 2013 at 7:45 PM, Mark Abraham wrote:
> Demux.pl pre-dates .cpt and -append. The only solution is to preserve your
Hello:
I am trying to compile gromacs with intel compiler. However, it failed
when I compile FFTW3 with command:
./configure --enable-sse --enable-float --with-pic --enable-single
--enable-static --enable-mpi --prefix=/home/albert/install/fftw-3.3.3
CC=icc CXX=icc F77=ifort
here is the l
Hi Albert,
one reason for the error you see could be that you are using a non-Intel
MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well.
Carsten
On Apr 5, 2013, at 12:25 PM, Albert wrote:
> Hello:
>
> I am trying to compile gromacs with intel compiler. However, it failed w
Hi,
On Thu, Apr 4, 2013 at 10:01 PM, Oleksandr Sushko
wrote:
> I'm want to analyse stratified layers of water around protein,
> so I provide next selection file to g_select:
[clip]
> (shell2 is supposed to be a layer of whole water molecules from the layer
> 3 to 4 A)
> but it doesn't work corre
On 4/5/13 6:38 AM, Carsten Kutzner wrote:
Hi Albert,
one reason for the error you see could be that you are using a non-Intel
MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well.
Is there any point in compiling FFTW in parallel? I have never once done it nor
found it ne
On 4/5/13 3:29 AM, Albert wrote:
Hello:
I am trying to do umbrella sampling for a protein/ligand water system these
days following Justin's nice tutorial. And I've got some questions:
(1) in the tutorial, the small peptide was pulling along Z direction. I am just
wondering, will the small p
On 4/5/13 4:23 AM, 라지브간디 wrote:
Dear gmx,
I understood that CHARMM supports two neutral/protonated histidine (HSD/HSE)
and fully protonated(HSP). How about the heme bound HIS version? I couldn't
find the HIS1 which knows as histidine bound to a heme? how do i link the heme
bound his using ch
On Apr 5, 2013, at 12:52 PM, Justin Lemkul wrote:
>
>
> On 4/5/13 6:38 AM, Carsten Kutzner wrote:
>> Hi Albert,
>>
>> one reason for the error you see could be that you are using a non-Intel
>> MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well.
>>
>
> Is there any point
Great.
Some of the data at the end of the .log file is easily recomputed from
the output at every exchange attempt once the .log files are
concatenated, but there will be loss of precision in re-computing the
average exchange acceptance probability, etc.
Mark
On Fri, Apr 5, 2013 at 10:37 AM, Joã
Teemu Murtola-3 wrote
> Hi,
>
> On Thu, Apr 4, 2013 at 10:01 PM, Oleksandr Sushko
> <
> o.sushko@.ac
> >wrote:
>
>> I'm want to analyse stratified layers of water around protein,
>> so I provide next selection file to g_select:
>
> [clip]
>> (shell2 is supposed to be a layer of whole water mol
So last week I read a post about liquid/gas layers in a box and it has me thinking (ie I cant shut it off). As it would sim wise (and I asume there is already something somewhere that does it) for a large body of fileds such as astrophysics, liquid dynamics, gas/gas interface I woundered if anyo
Hi all,
I am trying to simulate a system of protein and lipid bilayer ( in this case
POPC). The ff I am using is CHARMM36 and I used related settings from
literature.
I used InflateGRO to pack the lipids around my protein. Then put a position
restraint on my protein and P atoms of POPC. With
Hi all,
I have problem ruunning NVT with Z direction extended to get surface
tension of a polymer packed in a cell. I tried the same procedure for an
alkane and NVT works well however for the polymer the run crashes at the
very first step..
Doe anyone have clue what wrong could be? Many thanks.
On 04/05/2013 12:38 PM, Carsten Kutzner wrote:
Hi Albert,
one reason for the error you see could be that you are using a non-Intel
MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well.
Carsten
thanks a lot both Carsten and Justin.
I've compiled both fftw and openmpi with i
> Hi all,
>
> I have problem ruunning NVT with Z direction extended to get surface
> tension of a polymer packed in a cell. I tried the same procedure for an
> alkane and NVT works well however for the polymer the run crashes at the
> very first step..
>
> Doe anyone have clue what wrong could be?
I' d like to know if it is acceptable to change the molecule coordinates to
solve this problem?
Some time back, I deleted such a molecule and then I got a fatal error
containing that the trj file and other inputs are not inconsistent.
Would you please give me suggestions? I need them urgently.
Hi Vitaly,
To get surface tension one needs to extend Z to get a surface. From bulk it
is not possible to create a surface.
My problem is NVT crashes at step 0 and no energies or any other output
file is written...
On 5 April 2013 10:25, Dr. Vitaly Chaban wrote:
> > Hi all,
> >
> > I have pro
On Apr 5, 2013, at 4:21 PM, Albert wrote:
> On 04/05/2013 12:38 PM, Carsten Kutzner wrote:
>> Hi Albert,
>>
>> one reason for the error you see could be that you are using a non-Intel
>> MPI compiler wrapper. I think you need to specify MPICC=mpiicc as well.
>>
>> Carsten
>
>
> thanks a lot
On Fri, Apr 5, 2013 at 9:55 AM, Shima Arasteh
wrote:
>
>
> Hi all,
>
> I am trying to simulate a system of protein and lipid bilayer ( in this
> case POPC). The ff I am using is CHARMM36 and I used related settings from
> literature.
>
> I used InflateGRO to pack the lipids around my protein. Then
On Fri, Apr 5, 2013 at 10:27 AM, Shima Arasteh
wrote:
> I' d like to know if it is acceptable to change the molecule coordinates
> to solve this problem?
>
>
It's unlikely that some ad hoc change will magically fix a problem. Energy
minimization should take care of clashes.
> Some time back, I
Dear gmx users,
I could able to install gmx4.6.1 without MPI option in my cluster, whereas the
MPI fails to install and gives the following error ( used command line cmake ..
-DGMX_MPI=ON -DGMX_BUILD_OWN_FFTW=ON )
CMake Error at cmake/gmxManageMPI.cmake:161 (message):
MPI support requested
As I visualized the system, I see a water molecule somewhere between lipid
chains near the protein entrance. This has been happen during NPT. I' d like to
delete this molecule but with such a kind of fatal error this would impossible.
So what's the way? Is there any tricky way to change coordin
On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh
wrote:
> As I visualized the system, I see a water molecule somewhere between lipid
> chains near the protein entrance. This has been happen during NPT. I' d
> like to delete this molecule but with such a kind of fatal error this would
> impossible. S
On 04/05/2013 04:59 PM, Carsten Kutzner wrote:
Hm, this is another issue now. What version of the Intel compiler are you using?
With icc 13.0 it works for me, but I remember having problems with older
versions as well.
Carsten
I am using 2011 sp2 version. probably I should try the new one
> My problem is NVT crashes at step 0 and no energies or any other output
> file is written...
>
>
>
What about visualizing your interface?
> On 5 April 2013 10:25, Dr. Vitaly Chaban wrote:
>
>> > Hi all,
>> >
>> > I have problem ruunning NVT with Z direction extended to get surface
>> > t
You mean start over the NPT step?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul
To: Discussion list for GROMACS users
Cc:
Sent: Friday, April 5, 2013 7:50 PM
Subject: Re: Fw: [gmx-users] water molecule can not be settled
On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh
w
On Fri, Apr 5, 2013 at 11:22 AM, Shima Arasteh
wrote:
> You mean start over the NPT step?
>
>
Yes.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://w
Hi,
As the error message states, the reason for the failed configuration is
that CMake can't auto-detect MPI which is needed when you are not providing
the MPI compiler wrapper as compiler.
If you want to build with MPI you can either let CMake auto-detect MPI and
just compile with the C compiler
After having followed for longer time the queries sent by some Indian fellows,
I wonder if it wouldn't more effective to arrange for a GROMACS tutorial
offered by Justin in an Indian location. Maybe you, the Indian fellows, can
arrange for the financing and invite Justin to hold such a Tutorial
Hello:
I am trying to run umbrella sampling, the system contains a ligand.
here is the pulling setting:
; Pull code
pull= umbrella
pull_geometry = distance ; simple distance increase
pull_dim= Y N N
pull_start = yes ; define initial COM distance > 0
pull_ngro
Dear users
I have used AMBER MD package to run simulation for a solvent box. I am now
using the gromacs utility to calculate rdf as follows:
g_rdf -f file.trr -s file.pdb -n rdf.ndx -o rdf.xvg
However, I get no data in the output rdf.xvg. Since Im using specially
generated force field parameters
Hello:
I found that there would be some problem of genion in 4.6.1:
grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr
NOTE 1 [file complex.top, line 44008]:
System has non-zero total charge: -11.00
Total charge should normally be an integer. See
http://www.gromacs.org/Docum
Don't you have to give tyne name of the positive and negative ions that will be
added by genion? Otherwise, how would it know?
Warren Gallin
On 2013-04-05, at 1:05 PM, Albert wrote:
> Hello:
>
> I found that there would be some problem of genion in 4.6.1:
>
> grompp_mpi -f em.mdp -c solv.gr
On Fri, Apr 5, 2013 at 3:05 PM, Albert wrote:
> Hello:
>
> I found that there would be some problem of genion in 4.6.1:
>
> grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr
>
> NOTE 1 [file complex.top, line 44008]:
> System has non-zero total charge: -11.00
> Total charge sho
On Fri, Apr 5, 2013 at 3:05 PM, Albert wrote:
> Hello:
>
> I found that there would be some problem of genion in 4.6.1:
>
> grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr
>
> NOTE 1 [file complex.top, line 44008]:
> System has non-zero total charge: -11.00
> Total charge sho
On Fri, Apr 5, 2013 at 2:03 PM, Albert wrote:
> Hello:
>
> I am trying to run umbrella sampling, the system contains a ligand. here
> is the pulling setting:
>
> ; Pull code
> pull= umbrella
> pull_geometry = distance ; simple distance increase
> pull_dim= Y N N
> pull_sta
On 04/05/2013 09:09 PM, Warren Gallin wrote:
Don't you have to give tyne name of the positive and negative ions that will be
added by genion? Otherwise, how would it know?
Warren Gallin
No, it doesn't work either:
genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral
-norandom -p
On Fri, Apr 5, 2013 at 2:30 PM, Venkat Reddy wrote:
> Dear users
>
> I have used AMBER MD package to run simulation for a solvent box. I am now
> using the gromacs utility to calculate rdf as follows:
>
> g_rdf -f file.trr -s file.pdb -n rdf.ndx -o rdf.xvg
>
> However, I get no data in the output
On Fri, Apr 5, 2013 at 3:09 PM, Warren Gallin wrote:
> Don't you have to give tyne name of the positive and negative ions that
> will be added by genion? Otherwise, how would it know?
>
>
Default names are used (see genion -h), and the default names are correct
for all force fields as of version
> On 04/05/2013 09:09 PM, Warren Gallin wrote:
>> Don't you have to give tyne name of the positive and negative ions that
>> will be added by genion? Otherwise, how would it know?
>>
>> Warren Gallin
>
> No, it doesn't work either:
>
> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutra
Again and again posting from Abhishek Acharya or Shima, or Rama David or
somehow else ... pls read my posting before, it could be useful for you, Indian
fellows ... maybe it's possible to get some kind of agreement though
brahmin.net or so ..
Best regards of somebody experienced with Indian "sc
But you have conf.gro
On Fri, Apr 5, 2013 at 10:29 PM, Elisabeth wrote:
> Well I am not getting the trajectory. Simulation crashes before any step
> is calculated :(
>
>
> On 5 April 2013 11:20, Dr. Vitaly Chaban wrote:
>
>>
>>
>>> My problem is NVT crashes at step 0 and no energies or any oth
> Again and again posting from Abhishek Acharya or Shima, or Rama David or
> somehow else ... pls read my posting before, it could be useful for you,
> Indian fellows ... maybe it's possible to get some kind of agreement
> though brahmin.net or so ..
>
> Best regards of somebody experienced with In
The structure is taken from the end of previous simulation which terminates
successfully. The initial structure should not be the problem. What I do
only edit the last line (Z direction) of this structure to create vacuum.
This the output from log file.
Charge group distribution at step 0: 81 188
I'm running gromacs in parallel.I have 6 nodes.There are 96 cores. But hoiw
to reduce the load imbalance and improve the performance?
The PME-node is 16 and the PP-node is 80.How to divide?
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Ple
On Fri, Apr 5, 2013 at 10:03 PM, 陈照云 wrote:
> I'm running gromacs in parallel.I have 6 nodes.There are 96 cores. But hoiw
> to reduce the load imbalance and improve the performance?
> The PME-node is 16 and the PP-node is 80.How to divide?
>
Generally, if you're losing a lot of performance, mdru
Hi!
I have some questions.
1. Is there any method for me to improve my mdrun performance?
I have read the manual,and tested some option of mdrun,such as
-rdd,-rcon,-dds,-gcom. But they doesn't work. I have no idea about that.
2. Can gromacs 4.6.1 support K20?
I want to use CPU+GPU. But I met
On Fri, Apr 5, 2013 at 10:51 PM, 陈照云 wrote:
> Hi!
> I have some questions.
> 1. Is there any method for me to improve my mdrun performance?
> I have read the manual,and tested some option of mdrun,such as
> -rdd,-rcon,-dds,-gcom. But they doesn't work. I have no idea about that.
>
It is usua
Thank you Justin. I have now the topology. I have a quick question
regarding atom types. I used opls_143 and opls_144 for C and H of ethylene
respec in rtp. However, in VMD I dont see double bonds C=C. I though maybe
these are not the proper atomtypes for H2C=CH2.
rtp entry:
[ atoms ]
C1op
There was no fatal error preceding the output. After selecting the groups
following are the output on the screen
Reading frame 1 time0.100
Warning: can not make broken molecules whole without a run input file,
don't worry, mdrun doesn't write broken molecules
Reading frame20
Dear Specialists
I am a beginner at Gromacs. I work with MARTINI CG force field.
I selected 5 for
nstxout = 5
nstvout = 5
nstenergy = 5
nstlog = 5
nstxtcout = 5
and my jobs have been finished.
I found that this
Dear Gromacs Users!
I'm looking for cut-offs parameters which would be suitable for the
simulation of the membrane proteins (bergers united-atom lipids) with the
amber-99 force fields (full-atomic protein representation). I'd be thankful
to anyone who can provide me with such cut-offs for vdw as
You need to re submit the jobs, with decreased time.
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat, Apr 6, 2013 at 11:20 AM, dina dusti wrote:
> Dear Specialists
>
>
> I am a beginner at Gromacs. I work with MARTINI CG force field.
>
> I selected 5 for
>
> nstxout= 5
> nst
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