Dear gromacs users,
I have run a MD of 2 short peptides respectively, I want to compare the
flexibility between these two peptides along the full sequence via the
per-residue RMSF.
I understand that gmx rmsf computes the root mean square fluctuation of atomic
positions in the trajectory
Dear gromacs users,
I have run a MD of 2 short peptides respectively, I want to compare the
flexibility between these two peptides along the full sequence via the
per-residue RMSF.
I wonder that should I use "nofit" of "fit" option when I calculate the
per-residue RMSF of a trajectory
>
>If I understand correctly, it terminates at 0.99*t, t is the time you
>set in hour.
>In you case, you simulation should be terminated at 0.1*0.99 = 0.099 h,
>which is 5.94 minutes.
>
>PS: 0.1 h is not 10 minutes, but 6 minutes.
>
>All the best,
>Qinghua
>
>
Dear gromacs user,
The computing workstation I used has a limited time: 6 hours, namely
the REMD will be terminated after 6 hours. So I add option "-maxh 0.1" in the
MD commands to test. The md commands are as below:
mdrun_mpi -s remd_.tpr -multi 20 -replex 1000 -x remd_.xtc -cpo
ou rotated your initial system by
>90 degrees too. Which one is "right?"
>
>Mark
>
>On Wed, Nov 1, 2017 at 10:20 AM YanhuaOuyang <15901283...@163.com> wrote:
>
>> Dear gromacs user,
>>
>>
>>Today, I continue the MD twice in two direc
Dear gromacs user,
Today, I continue the MD twice in two directories from the same point of
the MD trajectory, for example 100ns, using the same CPU, same checkpoint file,
same serve node. To my surprise, the energy informations are different between
the two continued log ouput files,
Hi,
I have run a MD simulation and used gmx do_dssp to calculate the secondary
structure content. The output files are md_dssp.xpm and scount.xvg. I want to
know that each residue belongs to what kind of secondary structure for each
frame. But the scount.xvg output file only have the number
Dear Justin, Thank you very much. I get it now.Best
regards,Ouyang
At 2017-07-31 10:46:10, "Justin Lemkul" <jalem...@vt.edu> wrote:
>
>
>On 7/30/17 8:58 PM, YanhuaOuyang wrote:
>> Hi,
>> I have run a protein MD simulation and choose a force field "8:
Hi,
I have run a protein MD simulation and choose a force field "8: CHARMM27
all-atom force field (CHARM22 plus CMAP for proteins) ". I wonder that whether
the CHARMM27 all-atom force field here is equal to the CHARMM22/CMAP
--
Gromacs Users mailing list
* Please search the archive at
's what you already have. See
>http://www.gromacs.org/Documentation/How-tos/REMD#Post-Processing
>
>Mark
>
>On Thu, Jun 1, 2017 at 5:37 AM YanhuaOuyang <15901283...@163.com> wrote:
>
>> Hi,
>>I have run a 100ns-REMD of protein, which has 20 replicas (i.e.
>
Hi,
I have run a 100ns-REMD of protein, which has 20 replicas (i.e. remd1.xtc,
remd2.xtc, ..., remd20.xtc). I want to analyze a trajectory at specific
temperature such as a trajectory at experiment temperature 298K rather than
analyzing the continuous trajectory. I have known GROMACS
Hi,
I have run REMD for 80ns. But I can't restart the REMD. The errors are as
following:
Fatal error in MPI_Allreduce: Message truncated, error stack:
MPI_Allreduce(1339)...: MPI_Allreduce(sbuf=0x7fff4ac3fa90,
rbuf=0x29af530, count=4, MPI_FLOAT, MPI_SUM, comm=0x8400) fai
led
Hi,
I have run REMD for 80648ps. And I have to restart the REMD because of the
limited time of super-computing center. However it always failed to restart
from 80648ps. The errors are as following:
Fatal error in MPI_Allreduce: Message truncated, error stack:
so why not start closer
>to it?
>
>Mark
>
>On Mon, Mar 20, 2017 at 2:01 PM YanhuaOuyang <15901283...@163.com> wrote:
>
>> Hi,
>> I plan to run a REMD for a protein in explicit water. The temperature
>> is 300k-500k and there are 40 replicas.
>> I
Hi,
I plan to run a REMD for a protein in explicit water. The temperature is
300k-500k and there are 40 replicas.
I wander that are only the "ref-t" option in the equi_*.mdp files different
when equilibration stage ? what about gen-temp option. should I make the
gen-temp equal to ref-t
Hi,
I have a long trajectory , which is broken into 2 part because of disk
space : traj 1 is 0ns-213ns, the other traj 2 is 200ns-300ns. How to
concatenate this two trajectory into one single file trj 3(0ns-300ns) with
trjcat since they have overlapping times(200ns-214ns)? how can I keep
Hi,
I have 60 replicas simulated with REMD using gromacs. I demultiplex .xtc files
with demux.pl script. I know we can generate a continue coordinate trajectory
using "gmx trjcat" combined with "-demux replica_index.xvg" option. However I
am confused with using the option "-demux
Hi,
I want to perform a MD of an IDP, whose temperature is set to 380K. As we know,
the MD is equilibrated firstly at NVT, then at NPT ensemble and production
MD at NPT ensemble normally.
Does someone know whether the 380K-MD can only perform at NVT ensemble since
the temperature(380K) is
Hi,
I am running a REMD of a disordered protein, I visualized the trajectory in
VMD and I found that the protein is very close to the box edge.
Then I use "gmx mindist " to check if a protein has seen its periodic
image during simulation. When I used the command "gmx mindist -f
Hi,
I am running a REMD of a protein, which ranged from 270 to 500K in explicit
water model with 60 replicas, and I stop to analyse the REMD data after
running for 50ns. I use the demux.pl script to get the continue the coordinate
for each replica. Then I calculate the Rg value for each
ham <mark.j.abra...@gmail.com> 写道：
>
> Hi,
>
> On Sun, Jun 12, 2016 at 3:22 PM YanhuaOuyang <15901283...@163.com> wrote:
>
>> Dear Gromacs users,
>>
>> I want to extend my REMD simulation to another 2 ns after a short REMD is
>> completed with G
Dear Gromacs users,
I want to extend my REMD simulation to another 2 ns after a short REMD is
completed with Gromacs 5.0.2
my commands:
gmx convert-tpr -s previous.tpr -extend 2000 -o next.tpr
gmx mdrun -s next.tpr -cpi state.cpt -multi 30 -replex 1000 -reseed -1
I wonder if the option
?
> 在 2016年6月3日，上午5:50，Justin Lemkul <jalem...@vt.edu> 写道：
>
>
>
> On 6/2/16 10:55 AM, YanhuaOuyang wrote:
>> Dear Gromacs users,
>>
>> I am going to run a MD of a 20-residue protein which is phosphorylated on the
>> Serine and Threonine residues wit
Dear Gromacs users,
I am going to run a MD of a 20-residue protein which is phosphorylated on the
Serine and Threonine residues with AMBER ff99SB-ILDN force field using
Gromacs5.0. When I run gmx pdb2gmx and choose AMBER ff99SB-ILDN force field, it
appears:
fatal error: residues SEP not found
t; let "n++"
> fn=($line)
> fix_problems my.log fixed.log ${fn[0]} ${fn[1]} $STEP
> cp fixed.log fixed.log.${n}
> cp fixed.log my.log
> find_problems fixed.log
> cp problems problems.$n
> cp problems.init problems.init.$n
> cp z z.$n
> done
>
>
&
Dear Grimacs users,
I did use the equation:Ti=T0*ek*i to generate a temperature distribution,
after a 2-ns REMD, I check the md.log file. I find the average exchange ratio
for each replica is poor. the average exchange ratio is as below
Replica exchange statistics
Repl 499 attempts, 250 odd,
Hi, I have run a REMD, which including 46 replicas. I searched how to analyze
my REMD statistics, but I am still confused how to analyze my result; how to
generate a continuous a energy distribution curve; how to deal with 46 .log
files. It seems so complicated.
one of my md.log file is as
ed to compile GROMACS
> differently, with real MPI support. See
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdrun-features.html#running-multi-simulations
>
> Mark
>
> On Fri, May 13, 2016 at 9:47 AM YanhuaOuyang <15901283...@163.com> wrote:
>
>>
Hi,
I am running a REMD of a protein, when I submit "gmx mdrun -s md_0_${i}.tpr
-multi 46 -replex 1000 -reseed -1", it fails as the below
Fatal error:
mdrun -multi or -multidir are not supported with the thread-MPI library. Please
compile GROMACS with a proper external MPI library.
I have
Hi,
I am running a REMD with grimacs 5.0, I have 46 replica, 4 nodes, 16 cores per
node. how can I use my compute resource and what’s the command of “gmx mdrun”?
the command is below, I am not sure weather it is right
mpirun -np 4 -npme gmx mdrun -s md_01.tpr -multi 46 -replex 500 -reseed -1.
> On Tue, 26 Apr 2016 13:42 YanhuaOuyang <15901283...@163.com> wrote:
>
>> Thank you so much, but the latter one is only suitable for REMD in NPT
>> ensemble.
>>> 在 2016年4月26日，上午1:20，Christopher Neale <chris.ne...@alum.utoronto.ca> 写道：
>>>
ance.php
> Another example is here: http://folding.bmc.uu.se/remd/
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
> <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of YanhuaOuyang
> <15901283...@163.
Dear all,
I am going to run a REMD of a protein(explicit solvent) in NVT ensemble
with gromacs, but I have trouble in determining a optimum temperature
distribution.Can anybody know the ways to determine the temperature?
--
Gromacs Users mailing list
* Please search the archive at
Hi, I have a sequence of an intrinsically disordered protein, I have no idea
how to start my REMD with gromacs. e.g. how to convert my sequence into a pdb
file
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
34 matches
Mail list logo
