Re: [gmx-users] How to deal with unexpected reactions in umbrella sampling?

whether he delivered the code for 3D-WHAM or not > >Best, > >On Thu, Feb 20, 2020 at 2:58 AM Qing Lv wrote: > >> Dear Colleagues, >> >> >> I am doing an umbrella sampling of an enzymatic reaction using QM/MM. >> However, as the reaction coordinate exceeds a c

[gmx-users] How to deal with unexpected reactions in umbrella sampling?

Dear Colleagues, I am doing an umbrella sampling of an enzymatic reaction using QM/MM. However, as the reaction coordinate exceeds a certain value, an unexpected reaction, which is obviously unreasonable, often occurs during the umbrella sampling. So, how to deal with such problem? The only

Re: [gmx-users] Error bar for umbrella sampling?

н, 13 янв. 2020 г., 17:35 Qing Lv : > >> Dear All, >> >> >> I wonder if the error bars are necessary for umbrella sampling in PMF >> calculation? If yes, how should the error bars be calculated? Need I do 2~3 >> repeats (with different random initial velo

[gmx-users] Error bar for umbrella sampling?

Dear All, I wonder if the error bars are necessary for umbrella sampling in PMF calculation? If yes, how should the error bars be calculated? Need I do 2~3 repeats (with different random initial velocites assigned)? Thanks, Qing -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Is minimization and equilibration needed for umbrella sampling?

21:29:23, "Justin Lemkul" wrote: > > >On 1/10/20 11:02 AM, Qing Lv wrote: >> Dear Colleagues, >> >> >> I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic >> reaction. The initial coordinates (with solvents and ions) for each

[gmx-users] Is minimization and equilibration needed for umbrella sampling?

Dear Colleagues, I am doing a QM/MM umbrella sampling to calculate the PMF of an enzymatic reaction. The initial coordinates (with solvents and ions) for each sampling window were extracted from previous trajectories. The reaction coordinate (bond length difference) of each initial frame was

Re: [gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

e >e.g. because they have [defaults] sections. You can #include files, but >they have to follow the structure of the example in chapter 5 of the manual >(and every tutorial). Defaults, then atomtypes and parameters, then >moleculetypes, then system. > >Mark > >On Fri, Jun 23, 201

Re: [gmx-users] 5-letter atom names in topology files

At 2017-06-23 21:55:39, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 6/23/17 9:53 AM, Qing Lv wrote: >> I tried pdb2gmx -merge interactive or -chainsep interactive, but neither >> work... > >There is no chain information in a .gro so this approa

Re: [gmx-users] 5-letter atom names in topology files

I tried pdb2gmx -merge interactive or -chainsep interactive, but neither work... Qing At 2017-06-23 17:19:55, "Fitsiou, Eleni" wrote: >Hi , >Rename your chains and you could use -merge interactive and the -ter flag >Best >-- >Gromacs Users mailing list > >*

Re: [gmx-users] 5-letter atom names in topology files

ot; in PDB), pdb2gmx might regard all aminoacids as one single chain. Sorry for not having explained clearly in previous emails. Any suggestions? Many thanks, Qing At 2017-06-23 16:24:13, "Qing Lv" <lvqingjie...@163.com> wrote: >Dear Mark, > > >Actually I had t

Re: [gmx-users] 5-letter atom names in topology files

our >.pdb file, and then manually renaming atoms. > >Mark > >On Fri, Jun 23, 2017 at 3:55 AM Qing Lv <lvqingjie...@163.com> wrote: > >> Hi, >> >> >> Gromos 54a7 force field has built-in topologies for some small molecules, >> like ATP. In these top

Re: [gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

directive. P.S. My topology file includes ATP, Protein, and Mg2+. I tried to remove Mg2+ (probably inappropriate) but still got the same errors. Thanks, Qing At 2017-06-23 09:46:49, "Qing Lv" <lvqingjie...@163.com> wrote: >Dear All, > > >I am setting up

[gmx-users] 5-letter atom names in topology files

Hi, Gromos 54a7 force field has built-in topologies for some small molecules, like ATP. In these topologies, many atoms have names of up to 5 letters, such as AO1PA and AO2PB. However, PDB files seem do not support 5-letter atom names. So, if I name an atom "AO2PB" in PDB, it will be

[gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

Dear All, I am setting up a simulation of protein-ATP complex. I manually combined the coordinates and topologies of the protein and ATP together, and ran editconf and solvate successfully. However, when I ran grompp, errors occurred: Syntax error - File forcefield.itp, line 4 Last line read:

Re: [gmx-users] How to read .dat file

l.gromacs.org/programs/gmx-rms.html >You can have a look at rms.xvg file, it contains rmsd values. > >Best regards, >Dading Huang > > >On Wed, Jun 14, 2017 at 7:05 PM, Qing Lv <lvqingjie...@163.com> wrote: > >> I generated a .dat file with the following command:

[gmx-users] How to read .dat file

I generated a .dat file with the following command: gmx rms -s .pdb -f 1.xtc -f2 2.xtc -n index.ndx -o rms.xvg -m rms.xpm -bin rms.dat But how to read the binary file rms.dat? The reason is that, I found the lowest RMSD in RMSD matrix (rms.xpm) is 0.52 nm; how to know which frame in 1.xtc

Re: [gmx-users] Anyone use FMA (Functional Mode Analysis) ?

Thank you. I have just received the response from Dr. Jochen Hub and solved this problem.Qing At 2017-05-14 22:42:30, "Qing Lv" <lvqingjie...@163.com> wrote: >Hi Colleagues, > >I am trying to compile FMA (Functional Mode Analysis), developed by Dr. Jochen >Hub.

[gmx-users] Anyone use FMA (Functional Mode Analysis) ?

Hi Colleagues, I am trying to compile FMA (Functional Mode Analysis), developed by Dr. Jochen Hub. However, I met difficulties in the installation. According to the instructions, I installed Gromacs 4.0.5 (also tried 4.0.7) and the related libraries (libf2c, lapack, mpich, etc). Firstly, cmake

[gmx-users] Interactive Essential Dynamics (IED) installation: vmdnumpy module not available

Dear all, I am trying to compile IED (Interactive essential dynamics) according to the instructions of http://mccammon.ucsd.edu/ied/ However, I always got such errors: -- vmd > gopython Info) Starting Python... Traceback (most recent call last): File

Re: [gmx-users] How to write pull code in umbrella sampling

Thank you so much, Justin. I will look into PLUMED. Qing At 2017-04-08 19:05:28, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 4/8/17 1:46 AM, Qing Lv wrote: >> Thank you, Justin. >> >> >> My goal is to investigate the conformation transitio

Re: [gmx-users] How to write pull code in umbrella sampling

d I divide the loop into many small segments (pull-groups) and define the pull coordinates separately? This seems horrible... Thanks, Qing At 2017-04-08 09:06:46, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 4/7/17 8:56 PM, Qing Lv wrote: >> Dear Colleagues, >&g

[gmx-users] How to write pull code in umbrella sampling

can provide a template of pull code for such simulations? Thanks a lot Qing Lv -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)s

[gmx-users] GMX 2016 compiling problem (libgromacs.so.2.1.0: undefined reference to `GOMP_parallel')

Dear Colleagues, I am now compiling GMX 2016.1 on CentOS 6, with devtoolset-3 and -4. When executing 'make' , I got such errors: [ 98%] Building CXX object share/template/CMakeFiles/template.dir/template.cpp.o Linking CXX executable ../../bin/template ../../lib/libgromacs.so.2.1.0: undefined

[gmx-users] Problems of compiling GMX 2016.1 on CygWin

Hi, I am trying to compile GMX 2016.1 on CygWin, but failed. mkdir build cd build cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs2016.1 -DGMX_BUILD_OWN_FFTW=ON make /tmp/cctDFyCD.s: Assembler messages: /tmp/cctDFyCD.s:49: Error: invalid register for .seh_savexmm Makefile:745:

Re: [gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")

to happen if you built on a different >machine than you were running on... Does $builddir/bin/mdrun-test pass? >Does the terminal output mention SIMD? > >Mark > >On Fri, Feb 3, 2017 at 1:29 PM Qing Lv <lvqingjie...@163.com> wrote: > >> Mark, >> >> >>

Re: [gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")

lly, e.g. $builddir/bin/simd-test > >Mark > >On Fri, Feb 3, 2017 at 6:52 AM Qing Lv <lvqingjie...@163.com> wrote: > >> Thank you, Mark. I am now trying to install devtoolset-2. >> >> >> Regarding Cygwin version, I must clarify that, although the compila

Re: [gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")

ecommend leaving >the system libraries alone on redhat systems, and instead compiling with >the devtoolset packages. > >Thanks for the Cygwin report. People often report problems that look like >they come from broken systems, and we rarely hear of a resolution. > >Mark >

[gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")

Hi Colleagues, I am trying to build GMX 5.1.x (tried 5.1.4, 5.1.1, & 5.1) on a Redhat 6.5 server; I have updated GCC compiler and all dependent libraries (tried GCC 4.9.4 and GCC 6.3.0). (The built-in compiler of Redhat 6.5 is GCC 4.4.7, which is too old.) I used the commmand export CC=gcc

Re: [gmx-users] reproducibility of trajectory

observe yourself in a car crash every day, now you have evidence that you need driving lessons... If you had a car crash once every hundred days, and reported only that single day as evidence you need lessons... that'd be wrong on many levels. Mark On Wed, Aug 19, 2015 at 10:31 AM Qing Lv

[gmx-users] reproducibility of trajectory

Hi, I did a 200-ns MD for a protein and found an interesting conformation transition, and according to NMR study in literature, it is believed that 10 us ~ ms scale simulations are needed to get this conformation transition. However, when I tried to reproduce this conformation transition, I was

[gmx-users] reproducibility of trajectory

Hi, I did a 200-ns MD for a protein and found an interesting conformation transition, and according to NMR study in literature, it is believed that 10 us ~ ms scale simulations are needed to get this conformation transition. However, when I tried to reproduce this conformation transition, I was

Re: [gmx-users] How to justify when the trajectory reached equilibrium

I see. Thanks. Qing At 2015-07-11 05:07:27, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 11:00 PM, Qing Lv wrote: It means to evaluate quantities over successive blocks of time (e.g. using -b and -e that all GROMACS analysis tools support) and check to see whether

Re: [gmx-users] How to justify when the trajectory reached equilibrium

that will help? Best, Qing At 2015-07-09 19:41:09, Justin Lemkul jalem...@vt.edu wrote: On 7/8/15 9:48 PM, Qing Lv wrote: Hi, I did a 70-ns MD simulation. I wonder how to justify when the trajectory reached equilibrium... Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns

Re: [gmx-users] on trjconv command

Hi Brett, I think the following command will work: trjconv -f source.xtc -skip 5 -o target.xtc Qing At 2015-07-10 10:10:39, Brett brettliu...@163.com wrote: Dear All, Will you please show me the command based on the following cited content from the website on how to convert a xtc file with

Re: [gmx-users] How to justify when the trajectory reached equilibrium

need to divide in such an analysis? e.g., for a 100-ns trajectory, is it appropriate to divide it into 5-ns or 10-ns blocks to see if it has converged? Qing At 2015-07-10 01:39:42, Justin Lemkul jalem...@vt.edu wrote: On 7/9/15 10:11 AM, Qing Lv wrote: Thank you, Justin. I am trying

[gmx-users] How to justify when the trajectory reached equilibrium

Hi, I did a 70-ns MD simulation. I wonder how to justify when the trajectory reached equilibrium... Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns and kept stable after that. Could I justify that the system reached equilibrium at 12 ns? Are there any

[gmx-users] How to justify when the trajectory reached equilibrium

Hi, I did a 70-ns MD simulation. I wonder how to justify when the trajectory reached equilibrium... Seen from RMSD-time curve of C-alpha, the curve reached about 1 nm at 12 ns and kept stable after that. Could I justify that the system reached equilibrium at 12 ns? Are there any