[gmx-users] nonbonded molecules and atoms
Dear all, I am new to gromacs software. I was trying to make simple sodium nitrate (NaNO3) molecules. I have made .pdb file. then I got .gro file from pdb2gmx. But, I got struck in .itp file. Please help me. ( Na is nonbonded to any of N and O in NaNO3. And Na is also nonbonded to Na of 2nd NaNO3 molecule and so on). I have taken 50 NaNO3 molecules. Given below is .itp file, I cannot progress through grompp. as it is showing error as syntax error at '1 2 yes 1.0 1.0'. If possible correct my .itp file. [ defaults ] ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 [ moleculetype ] ; molname nrexcl NaN 4 [ atomtypes ] ;name atnum mass charge ptype sigma epsilon Na 11 22.98977 1.000 A 3.33045e-01 1.15980e-02 O 8 15.99940 -0.598 A 2.86000e-01 8.78640e-01 O 8 15.99940 -0.598 A 2.86000e-01 8.78640e-01 O 8 15.99940 -0.598 A 2.86000e-01 8.78640e-01 N 7 14.00670 0.794 A 3.15000e-01 7.11280e-01 [ nonbond_params ] ;i j func sigma epsilonNa Na 1 3.33045e-01 3.33045e-01 Na O 1 3.33045e-01 1.15980e-02 Na N 1 3.33045e-01 1.15980e-02 [ constraints ] ; ai aj funct b0 [exclusions ] 1 2 1 3 1 4 1 5 Waiting for kind reply,Thank you, With Regards, SUMAIR FAISAL AHMED. -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] fatal error invalid pairs 5
On 10/6/16 3:20 PM, Devon Dillon wrote: this is my error message -- Program gmx, VERSION 5.0.2 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-5.0.2/src/gromacs/gmxpreprocess/topdirs.c, line: 166 Fatal error: Invalid pairs type 5 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- help please and thank you : ) If this file came directly from ATB and you didn't touch it, contact the ATB developers, because they need to know that they're producing nonfunctional files. The only acceptable pair function types are 1 and 2. If you modified the file in any way, throw out what you did, familiarize yourself with Chapter 5 and what's acceptable in a topology, and start again. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs GMX_BUILD_FFTW warning in building Gromas 5.0.4
On 10/6/16 1:34 PM, Steve Seibold wrote: HelloI have been attempting to compile and build Gromacs 5.0.4for a couple of weeks. I have been following the instructions (having also readGromacs 5.0 instruction in Manual..) at https://ourphysics.org/wiki/index.php/How_to_compile_Gromacs#Gromacs_5.1.1_MPI.2C_single Specifically, I have used “Gromacs 5.0.4 MPI, Single, GPU”instructions at this site; however, without the “GPU” part.. I have both OpenMPI and FFTW-3.2.2 in the standardlocations. In the screen output when I use CMake to compile, I get the message that “can’t locate fftw3fmodule” . However, the configurations is done and the build files are made;however, I also get the message “CMake warning that manually-specified variableswere not use by the project: GMX_BUILD_FFTW” Does this mean FFTW is disabled? Not sure.. I made sure that I was using the correct version of CMakewhich is CMake-3.5.2 and the correct FFTW-3.2.2,,, I did find on line where someone online said if they reconfiguredFFTW with "--enable-float" that theysolved the problem of “can’tlocate fftw3f module”; but this was for Gromacs 4.5 and there is no realexplanation. So, I am hesitant to try this….. Any information would be extremely helpful!!! Thanks Steve Please make sure your emails have sensible line breaks; this is very hard to read. What you're observing is that "GMX_BUILD_FFTW" is not a valid argument. It's "GMX_BUILD_OWN_FFTW" and that's only needed if you want GROMACS to build FFTW for you. Since you already built FFTW (although 3.2.2 is utterly ancient, so you should get the latest version, i.e. 3.3.5) then you don't need this option. This is confirmed by the fact that, as you say, configuration completes. If cmake can't find a suitable FFTW, it will throw a fatal error. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] fatal error invalid pairs 5
this is my error message -- Program gmx, VERSION 5.0.2 Source code file: /home/abuild/rpmbuild/BUILD/gromacs-5.0.2/src/gromacs/gmxpreprocess/topdirs.c, line: 166 Fatal error: Invalid pairs type 5 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- help please and thank you : ) -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] high-temperature MD
Depends, actually. There are reasons one might want to simulate a system at 380 K in NVT using the average box volume from the 300 K NPT simulation. Temperature replica exchange typically employs NVT and so might other temperature-based enhanced sampling approaches. Justin's right, you have to think it through, but I'm just chiming in to suggest that the answer is not obvious from this thread thus far. TIP3P water doesn't boil in NPT until somewhere around 550 K, so NPT at 380 K is certainly possible. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul Sent: 06 October 2016 09:34:49 To: gmx-us...@gromacs.org Subject: Re: [gmx-users] high-temperature MD On 10/6/16 8:54 AM, OuyangYanhua wrote: > Dear Justin, >> > I had run a 300K-MD, now I want to run a high-temperature(380K) MD to compare > with the 300K-MD. > The 300K is first equilibrated at NVT, then at NPT and production MD at NPT. > So I want to know the high-temperature(380K) MD should run the same as the > 300k, which means the 380k is also first equilibrated at NVT, then at NPT and > production MD at NPT ensemble. > Think scientifically. If you only want to vary the temperature, does it make any sense to vary the simulation protocol? -Justin > Best regards, > Ouyang > >> 在 2016年10月6日，下午7:22，Justin Lemkul 写道： >> >> >> >> On 10/6/16 3:52 AM, YanhuaOuyang wrote: >>> 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 a high >>> temperature? Should I run the MD(380K) at NPT ensemble or at NPT ensemble? >>> >> >> 380 K is not very high. What you choose to do needs to be based on whatever >> real-world conditions you want to model. >> >> -Justin >> >> -- >> == >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> == >> -- >> 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)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. > > -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_spatial Problem
This works for me (careful with line wrapping if this email or the list mangles
it):
#!/bin/bash
PATH=/project2/p/pomes/cneale/GPC/exe/intel/gromacs-4.6.7/exec/bin:$PATH
export
GMXLIB=/project2/p/pomes/cneale/GPC/exe/intel/gromacs-4.6.7/exec/share/gromacs/top
# setup variables
CENTRAL="CHO"
SDF="CHL"
top=topology.top
gro=bath_298K.part0001.gro
xtc=bath_298K.part0001.xtc
# generate a .tpr file because one was not provided in the tarball
cp itp\ files/* .
rm -f this.tpr mdout.mdp
touch empty.mdp
grompp -f empty.mdp -p $top -c $gro -o this.tpr -maxwarn 1
# make the index file
clist=$(grep $CENTRAL $gro|awk '{print $1}'|sed "s/$CENTRAL//"|uniq)
{
for i in $clist; do
echo "r $i"
echo "r $i || \"$SDF\""
done
echo q
} > my.input
rm -f index.ndx
cat my.input | make_ndx -f $gro -o index.ndx
# create the independent segments
mkdir -p BITS
for i in $clist; do
rm -f BITS/central_${i}.xtc
echo -e "r_${i}\nr_${i}_${SDF}\n"| trjconv -f $xtc -s this.tpr -o
BITS/central_${i}.xtc -pbc atom -center -n index.ndx
done
# join the segments
rm -f tot.xtc
trjcat -f $(for i in $clist; do echo -n "BITS/central_${i}.xtc "; done) -o
tot.xtc -cat -nosort -keeplast
# create a gro for the new file type
i=$(echo $clist|head -n 1|awk '{print $1}')
rm -f onecentral.gro
echo -e "r_${i}\nr_${i}_${SDF}\n"| trjconv -f $gro -s this.tpr -o
onecentral.gro -pbc mol -center -n index.ndx
# make a new .ndx file
rm -f index2.ndx
echo q | make_ndx -f onecentral.gro -o index2.ndx
# process this trajectory for fitting
rm -f tot_fitted.xtc
echo -e "${CENTRAL}\nSystem\n" | trjconv -f tot.xtc -fit rot+trans -s
onecentral.gro -pbc none -n index2.ndx -o tot_fitted.xtc
## make the SDF
rm -f grid.cube
echo -e "${SDF}\n${CENTRAL}\n" | g_spatial -f tot_fitted.xtc -s onecentral.gro
-nab 100
## Run VMD. Load grid.cube as isosurface and onecentral.gro to show your
choline.
## Note the ability to use surface or grid representations for the isosurface.
The "points" representation is kind of useless.
I will send you an image of the SDF that I generated off list.
Good luck,
Chris.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Rubaiyet
Abedin
Sent: 05 October 2016 15:58:14
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] g_spatial Problem
Dear Dr. Neale,
Please find the following link of dropbox that contains the files.
https://www.dropbox.com/sh/ifeaegequznnbgg/AABO9AzE3PrbNtGfgMike0tWa?dl=0
Please let me know if you need anything else. I really appreciate your help.
Rubaiyet
On Wed, Oct 5, 2016 at 1:01 AM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> sent a reply previously, but looks like it was lost on my end.
>
> make a tarball of .gro .top all .itp and a small .xtc (5 frames) and post
> it somewhere and put a link on this list. Add a description of which
> molecule you want for central solute and what you want to make the SDF for.
> I will then take a look and post a script to make the SDF.
>
> Chris.
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Rubaiyet
> Abedin
> Sent: 04 October 2016 23:45:31
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] g_spatial Problem
>
> Dear Dr. Neale,
>
> Thanks for your reply. Actually my system is quite a big system. It
> contains:
>
> Cation - 250 molecules
> Anion - 250 molecules
> Type A (urea)- 500 molecules
> Type B (refrigerant)- 250 molecules
>
> I want to get spatial distribution function like the following. I used this
> picture as because this system is similar to mine:
> https://s26.postimg.org/hmw56k5d5/demo.jpg
>
> Let's say I am trying to get the sdf of anions around the cation (solute).
> When I am going through the manual of g_spatial, it did not specify I have
> to choose a single atom of solute. So first I took all the molecules of
> cation as a centered group and followed the steps that I mentioned in the
> earlier mail. I got something like this:
> https://s26.postimg.org/4794h3wvd/image.jpg
> If I load both grid files, it turned out like this :
> https://s26.postimg.org/hpg0te90p/image.jpg
>
> First of all it's rectangular, and all the sdf that I saw in the paper are
> spherical and in the center there are only one molecule (which is clearly
> different from mine).
>
> In the forum, I read that there should be only one centered molecule. So I
> made an index file including a random molecule of Cation and followed the
> steps. This time I got the image like this:
> https://s26.postimg.org/7gs51bacp/25percent_Copy.jpg
>
> So I am not sure what I am doing wrong. I tried to look for help. But I
> could not find any till now. Right now I am completely stuck.
>
> The process you said- to make 10 separate trajectories, in my case there
> are 250 molecules of solute and I have to do 250 analysis and then
> concatenate all the trajectories? I am not clear about
[gmx-users] Gromacs GMX_BUILD_FFTW warning in building Gromas 5.0.4
HelloI have been attempting to compile and build Gromacs 5.0.4for a couple of weeks. I have been following the instructions (having also readGromacs 5.0 instruction in Manual..) at https://ourphysics.org/wiki/index.php/How_to_compile_Gromacs#Gromacs_5.1.1_MPI.2C_single Specifically, I have used “Gromacs 5.0.4 MPI, Single, GPU”instructions at this site; however, without the “GPU” part.. I have both OpenMPI and FFTW-3.2.2 in the standardlocations. In the screen output when I use CMake to compile, I get the message that “can’t locate fftw3fmodule” . However, the configurations is done and the build files are made;however, I also get the message “CMake warning that manually-specified variableswere not use by the project: GMX_BUILD_FFTW” Does this mean FFTW is disabled? Not sure.. I made sure that I was using the correct version of CMakewhich is CMake-3.5.2 and the correct FFTW-3.2.2,,, I did find on line where someone online said if they reconfiguredFFTW with "--enable-float" that theysolved the problem of “can’tlocate fftw3f module”; but this was for Gromacs 4.5 and there is no realexplanation. So, I am hesitant to try this….. Any information would be extremely helpful!!! Thanks Steve -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun don't write a checkpoint file
Thank You Justin I run a short equilibration on my system and now I get the checkpoint file. Simon Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se im Auftrag von Justin Lemkul Gesendet: Donnerstag, 6. Oktober 2016 15:33 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] mdrun don't write a checkpoint file You're doing energy minimization. There is no checkpointing in EM. As an aside, you also did not provide accurate information in your previous message. You said you were using 5.1 but your .log indicates you are using 2016, and your command line was different. While it didn't matter here, please *always* provide accurate information to reach a resolution as quickly as possible. Had there been some problem, we would have tried to reproduce it with 5.1, which would have been entirely unproductive. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mail regarding installation of geomacs5.1.2
On 10/6/16 9:13 AM, subramanian vidhyasankar wrote: Dear mark and justin sir Thank you for your previous reply I installed successfully the gromacs5.1.2 But my bin directory does not contain any executable files *it contains tool gmx_d only* When i run the following command *./gmx_d g_select_d -h* i got the error as follows *Segmentation fault (core dumped)* i have used the following commands while configuring * cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs512 -DGMX_DOUBLE=on* make make install it would be helpful what mistake i have committed during installation Please search the archive and read the release notes. This exact topic came up just a few days ago. My tutorials have also been updated for the tool name changes that were introduced in 5.0 and made permanent in 5.1. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] high-temperature MD
On 10/6/16 8:54 AM, OuyangYanhua wrote: Dear Justin, I had run a 300K-MD, now I want to run a high-temperature(380K) MD to compare with the 300K-MD. The 300K is first equilibrated at NVT, then at NPT and production MD at NPT. So I want to know the high-temperature(380K) MD should run the same as the 300k, which means the 380k is also first equilibrated at NVT, then at NPT and production MD at NPT ensemble. Think scientifically. If you only want to vary the temperature, does it make any sense to vary the simulation protocol? -Justin Best regards, Ouyang 在 2016年10月6日，下午7:22，Justin Lemkul 写道： On 10/6/16 3:52 AM, YanhuaOuyang wrote: 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 a high temperature? Should I run the MD(380K) at NPT ensemble or at NPT ensemble? 380 K is not very high. What you choose to do needs to be based on whatever real-world conditions you want to model. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun don't write a checkpoint file
On 10/6/16 8:23 AM, Menig, Simon wrote: Thank you for your fast answer Justin I looked up the log files but I found no error and my disc space is sufficient and the simulation seem to end normal. Could the Problem be that my Simulation time is shorter than 15 min (max 5000 steps) ? (Shouldn't it write a cpt file after the End of the simulation) Parts of my log file: Log file opened on Thu Oct 6 14:09:27 2016 Host: linux-286u pid: 4384 rank ID: 0 number of ranks: 1 :-) GROMACS - gmx mdrun, 2016 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton FeenstraGerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios Karkoulis Peter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2015, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2016 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/simon/simu_test_cg/build_cg_membrane_test1 Command line: gmx mdrun -s input/ab26_wt_POPE_POPG_cg_eqi_1.tpr -o out_trr/ab26_wt_POPE_POPG_cg_eqi_1.trr -c output/ab26_wt_POPE_POPG_cg_eqi_1.gro -e output/ab26_wt_POPE_POPG_cg_eqi_1.edr -g output/ab26_wt_POPE_POPG_cg_eqi_1.log -cpo output/ab26_wt_POPE_POPG_cg_eqi_1 -v -cpt 1 GROMACS version:2016 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support:disabled SIMD instructions: AVX_256 FFT library:fftw-3.3.4-sse2-avx RDTSCP usage: enabled TNG support:enabled Hwloc support: disabled Tracing support:disabled Built on: Do 1. Sep 09:46:51 CEST 2016 Built by: simon@linux-286u [CMAKE] Build OS/arch: Linux 4.1.12-1-default x86_64 Build CPU vendor: Intel Build CPU brand:Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz Build CPU family: 6 Model: 45 Stepping: 7 Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU 4.8.5 C compiler flags:-mavx -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /usr/bin/c++ GNU 4.8.5 C++ compiler flags: -mavx-std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast Running on 1 node with total 4 cores, 8 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz Family: 6 Model: 45 Stepping: 7 Features: aes apic avx clfsh cmov cx8 cx16 htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic SIMD instructions most likely to fit this hardware: AVX_256 SIMD instructions selected at GROMACS compile time: AVX_256 Hardware topology: Basic Sockets, cores, and logical processors: Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7] - Energies (kJ/mol) Bond G96AngleProper Dih.LJ (SR) Coulomb (SR) 1.36475e+042.16816e+041.59230e+03 -2.94378e+06 -2.60982e+04 Potential Pressure (bar) Constr. rmsd -2.93295e+06 -8.86450e+015.54635e-06 Steepest Descents converged to Fmax < 100 in 3325 steps Potential Energy = -2.9329548e+06 Maximum force = 9.9675224e+01 on atom 3030 Norm of force = 3.0542336e+00 You're doing energy minimization. There is no checkpointing in EM. As an aside, you also did not provide accurate information in your previous message. You said you were using 5.1 but your .log indicates you are using 2016, and your command line was different. While it didn't matter here, please *always* provide accurate information to reach a resolution as quickly as possible. Had there been some problem, we would have tried to reproduce it with 5.1, which would have been entirely unproductive. -Just
[gmx-users] mail regarding installation of geomacs5.1.2
Dear mark and justin sir Thank you for your previous reply I installed successfully the gromacs5.1.2 But my bin directory does not contain any executable files *it contains tool gmx_d only* When i run the following command *./gmx_d g_select_d -h* i got the error as follows *Segmentation fault (core dumped)* i have used the following commands while configuring * cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs512 -DGMX_DOUBLE=on* make make install it would be helpful what mistake i have committed during installation with regards S.Vidhyasankar -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] high-temperature MD
Dear Justin, > I had run a 300K-MD, now I want to run a high-temperature(380K) MD to compare with the 300K-MD. The 300K is first equilibrated at NVT, then at NPT and production MD at NPT. So I want to know the high-temperature(380K) MD should run the same as the 300k, which means the 380k is also first equilibrated at NVT, then at NPT and production MD at NPT ensemble. Best regards, Ouyang > 在 2016年10月6日，下午7:22，Justin Lemkul 写道： > > > > On 10/6/16 3:52 AM, YanhuaOuyang wrote: >> 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 a high >> temperature? Should I run the MD(380K) at NPT ensemble or at NPT ensemble? >> > > 380 K is not very high. What you choose to do needs to be based on whatever > real-world conditions you want to model. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] mdrun don't write a checkpoint file
Thank you for your fast answer Justin I looked up the log files but I found no error and my disc space is sufficient and the simulation seem to end normal. Could the Problem be that my Simulation time is shorter than 15 min (max 5000 steps) ? (Shouldn't it write a cpt file after the End of the simulation) Parts of my log file: Log file opened on Thu Oct 6 14:09:27 2016 Host: linux-286u pid: 4384 rank ID: 0 number of ranks: 1 :-) GROMACS - gmx mdrun, 2016 (-: GROMACS is written by: Emile Apol Rossen Apostolov Herman J.C. BerendsenPar Bjelkmar Aldert van Buuren Rudi van Drunen Anton FeenstraGerrit Groenhof Christoph Junghans Anca HamuraruVincent Hindriksen Dimitrios Karkoulis Peter KassonJiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Magnus Lundborg Pieter MeulenhoffErik Marklund Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman Teemu Virolainen Christian WennbergMaarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2015, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. GROMACS: gmx mdrun, version 2016 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/simon/simu_test_cg/build_cg_membrane_test1 Command line: gmx mdrun -s input/ab26_wt_POPE_POPG_cg_eqi_1.tpr -o out_trr/ab26_wt_POPE_POPG_cg_eqi_1.trr -c output/ab26_wt_POPE_POPG_cg_eqi_1.gro -e output/ab26_wt_POPE_POPG_cg_eqi_1.edr -g output/ab26_wt_POPE_POPG_cg_eqi_1.log -cpo output/ab26_wt_POPE_POPG_cg_eqi_1 -v -cpt 1 GROMACS version:2016 Precision: single Memory model: 64 bit MPI library:thread_mpi OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support:disabled SIMD instructions: AVX_256 FFT library:fftw-3.3.4-sse2-avx RDTSCP usage: enabled TNG support:enabled Hwloc support: disabled Tracing support:disabled Built on: Do 1. Sep 09:46:51 CEST 2016 Built by: simon@linux-286u [CMAKE] Build OS/arch: Linux 4.1.12-1-default x86_64 Build CPU vendor: Intel Build CPU brand:Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz Build CPU family: 6 Model: 45 Stepping: 7 Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU 4.8.5 C compiler flags:-mavx -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /usr/bin/c++ GNU 4.8.5 C++ compiler flags: -mavx-std=c++0x -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast Running on 1 node with total 4 cores, 8 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz Family: 6 Model: 45 Stepping: 7 Features: aes apic avx clfsh cmov cx8 cx16 htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic SIMD instructions most likely to fit this hardware: AVX_256 SIMD instructions selected at GROMACS compile time: AVX_256 Hardware topology: Basic Sockets, cores, and logical processors: Socket 0: [ 0 4] [ 1 5] [ 2 6] [ 3 7] - Energies (kJ/mol) Bond G96AngleProper Dih.LJ (SR) Coulomb (SR) 1.36475e+042.16816e+041.59230e+03 -2.94378e+06 -2.60982e+04 Potential Pressure (bar) Constr. rmsd -2.93295e+06 -8.86450e+015.54635e-06 Steepest Descents converged to Fmax < 100 in 3325 steps Potential Energy = -2.9329548e+06 Maximum force = 9.9675224e+01 on atom 3030 Norm of force = 3.0542336e+00 M E G A - F L O P S A C C O U N T I N G NB=Group-cutoff nonbonded kernelsNxN=N-by-N cluster Verlet kernels RF=Reaction-Field VdW=Van der Waals QSTab=quadratic-spline table W3=SPC/TIP3p W4=TIP4p (single or pairs) V&F=Potential and force V=Potential only F=Force only Computing: M-Number M-Flops % Flops - Pair Search distance check 38504.672646 346542.05416.3 NxN RF Elec. + LJ
Re: [gmx-users] mdrun don't write a checkpoint file
On 10/6/16 7:41 AM, Menig, Simon wrote: Hi, I am new to GROMACS and I wanted to run a Coars-Grain simulation but gmx mdrun doesn't write a checkpoint file and I found no solution for my Problem in the Docs or Internet. I hope someone can help me with this problem, I need this files for extending my Simulation (similar to Lysozyme tutorial) . I use GROMACS 5.1, the mdrun command I used is: gmx mdrun -s input/name.tpr -o out_trr/name.trr -c output/name.gro -e output/name.edr -g output/name.log -cpo output/name.cpt I also tried the -deffnm option Could this be a bug or is another parameter needed (tried -cpt option) ? That command should produce a checkpoint file every 15 minutes, which is the default behavior. The only reasons that it wouldn't be written are if the run terminated abnormally or if you ran out of disk space. Either way, the .log file or stderr/stdout should have informative information. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Different Results with Different Platforms
Thank you very much, Justin. I was take note of this in subsequent runs. Thank you so, so much for your assistance. It is greatly appreciated! -- Best wishes, Kelechi -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] mdrun don't write a checkpoint file
Hi, I am new to GROMACS and I wanted to run a Coars-Grain simulation but gmx mdrun doesn't write a checkpoint file and I found no solution for my Problem in the Docs or Internet. I hope someone can help me with this problem, I need this files for extending my Simulation (similar to Lysozyme tutorial) . I use GROMACS 5.1, the mdrun command I used is: gmx mdrun -s input/name.tpr -o out_trr/name.trr -c output/name.gro -e output/name.edr -g output/name.log -cpo output/name.cpt I also tried the -deffnm option Could this be a bug or is another parameter needed (tried -cpt option) ? Thanks Simon -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Fatal error Invalid pairs 5
On 10/5/16 11:26 PM, Devon wrote: I'm having big problems. I generated a topology using atb. I'm using the external force fields recommended. I'm getting an invalid pairs 5 error. It would be greatly appreciated if someone could help alleviate some stress. Thank you Please provide a full error message, copied and pasted from your terminal, the command(s) used, and any relevant snippets of the files that correspond to offending lines. ATB is a heavily used and well tested server; if it has generated syntactically incorrect files without any further user manipulation, this would be very odd. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] high-temperature MD
On 10/6/16 3:52 AM, YanhuaOuyang wrote: 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 a high temperature? Should I run the MD(380K) at NPT ensemble or at NPT ensemble? 380 K is not very high. What you choose to do needs to be based on whatever real-world conditions you want to model. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Different Results with Different Platforms
On 10/6/16 7:13 AM, Kelechi Okoroafor wrote: Thank you for the tip, Justin. I incorrectly thought that the coordinates and box dimensions were sufficient to preserve the pressure of the system. I shall make a habit of restarting simulations with the checkpoint file rather than .gro files. My sequence of commands were: - gmx grompp -f npt.mdp -c EM.gro -p sys.top -o NPT1.tpr -n index.ndx -maxwarn -1 - gmx mdrun -v -deffnm NPT1 -nb gpu -tunepme - gmx editconf -f NPT1.gro -o NPT1.pdb -c -d 0.00 - gmx editconf -f NPT1.pdb -o NPT1.gro -c -d 0.00 - If you just want to convert file formats, omit -c -d in your editconf command and nothing will change. By using -d 0.00, you will be adjusting the system size (you will see this by comparing the box vectors in the input and output files). You're ensuring a bad discontinuity by doing this. My recommendation is to always use unmodified files when continuing runs; it's basically bulletproof. If you want a different format for visualization, that's fine, but just use it for visualization. Your original NPT1.gro should have been fine, but having transformed to .pdb while manipulating the box, then back, you're just invalidating anything that was done previously. -Justin gmx grompp -f pme.mdp -c NPT1.gro -p sys.top -o NVT1.tpr -n index.ndx -maxwarn -1 - gmx mdrun -v -deffnm NVT1 -nb gpu -tunepme -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Different Results with Different Platforms
Thank you for the tip, Justin. I incorrectly thought that the coordinates and box dimensions were sufficient to preserve the pressure of the system. I shall make a habit of restarting simulations with the checkpoint file rather than .gro files. My sequence of commands were: - gmx grompp -f npt.mdp -c EM.gro -p sys.top -o NPT1.tpr -n index.ndx -maxwarn -1 - gmx mdrun -v -deffnm NPT1 -nb gpu -tunepme - gmx editconf -f NPT1.gro -o NPT1.pdb -c -d 0.00 - gmx editconf -f NPT1.pdb -o NPT1.gro -c -d 0.00 - gmx grompp -f pme.mdp -c NPT1.gro -p sys.top -o NVT1.tpr -n index.ndx -maxwarn -1 - gmx mdrun -v -deffnm NVT1 -nb gpu -tunepme -- Best wishes, Kelechi -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] PMF of a short peptide on a solid surface
Dear gromacs user, In order to simulate the PMF of a adsorbed short peptide on a solid surface, first I minimised and equlibrated(NVT and NPT) the system and then I did a 60 ns of production run in which the peptide fully adsorbed to the surface. I used these out put to pull away the peptide from the surface using below mdp file (to produced required trajectory for generating configuration): +++ title= C16-Slab-Water-Na integrator = md dt= 0.001 ; 1 fs nsteps= 1000 ; 10 ns xtc-precision = 2000 nstenergy= 5000 nstlog = 5000 nstxout-compressed = 1000 nstxout = 1000 nstlist = 40 continuation = yes gen-vel = no ;gen-temp = 298.15 ;gen-seed = 173529 constraint-algorithm = lincs constraints = h-bonds cutoff-scheme= Verlet coulombtype = PME rcoulomb = 1.3 vdwtype = Cut-off rvdw = 1.3 DispCorr = EnerPres tcoupl = Nose-Hoover ;v-rescale ;berendsen tc-grps = Protein Non-Protein tau-t= 1.61 1.61 ref-t= 298.15 298.15 nhchainlength= 1 pbc = xyz pcoupl = no energygrps= Protein Slab Water_and_ions pull = yes pull-ngroups = 2 pull-ncoords = 1 pull-group1-name = Protein pull-group2-name = Slab pull-coord1-groups = 1 2 pull-coord1-type = umbrella pull-coord1-dim = N N Y pull-coord1-start= yes pull-coord1-rate = 0.001 ;;;0.007 pull-coord1-vec = 0.0 0.0 1.0 pull-coord1-geometry = direction-periodic pull-coord1-k= 500 ;;;1000 pull-print-components= Yes Although I do not use hard spring (500 and 1000) and fast pulling rate(0.001 and 0.007) but I do not know why the peptide suddenly pulled away from the slab in the second or third frame? Thanks. Alex -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Replica Exchange MD
Thank you very much for your reply and suggestions. I am discussing with system admin regarding this issue. With Best Regards, Kalyanashis Jana On Wed, Oct 5, 2016 at 6:01 PM, Mark Abraham wrote: > Hi, > > On Wed, Oct 5, 2016 at 2:17 PM Kalyanashis Jana > wrote: > > > Hi Mark, > > The MD run stopped after 52.9 ps and the error is > > "MPI: STDOUT or STDERR buffer exhausted. > > MPI: Set MPI_UNBUFFERED_STDIO or output no more than about 8192 > characters > > MPI: between newlines > > > Your MPI library makes assumptions about the MPI application that are > inappropriate. mdrun expects to be able to write to stdout and it works > like stdout. > > Either set the MPI_UNBUFFERED_STDIO variable like it suggests (please talk > to your sysadmins and/or documentation for how to do this, I have no idea, > and little interest in SGI's MPI implementation that causes me as many > problems as all the other implementations put together :-)), or use any > other MPI library you have available. > > Mark > > > > /opt/sgi/mpt/mpt-2.01/bin/mpiexec_mpt: line 52: 29708 Killed > >$mpicmdline_prefix -f $paramfile" > > > > > > I have pasted the equil.mdp, more less similar to the REMD tutorial, for > > your kind perusal. > > > > > > include = > > define = > > integrator = md > > tinit= 0 > > dt = 0.001 > > nsteps = 50 > > init-step= 0 > > simulation-part = 1 > > comm-mode= Linear > > nstcomm = 100 > > comm-grps= > > bd-fric = 0 > > ld-seed = 1993 > > emtol= 10 > > emstep = 0.01 > > niter= 20 > > fcstep = 0 > > nstcgsteep = 1000 > > nbfgscorr= 10 > > rtpi = 0.05 > > nstxout = 250 > > nstvout = 1000 > > nstfout = 0 > > nstlog = 100 > > nstcalcenergy= 100 > > nstenergy= 1000 > > nstxtcout= 0 > > xtc-precision= 1000 > > xtc-grps = > > energygrps = > > ;cutoff-scheme= Verlet > > nstlist = 10 > > ns-type = Grid > > pbc = xyz > > periodic-molecules = no > > ;verlet-buffer-drift = 0.005 > > rlist= 1 > > rlistlong= -1 > > ;nstcalclr= -1 > > coulombtype = PME > > ;coulomb-modifier = Potential-shift-Verlet > > rcoulomb-switch = 0 > > rcoulomb = 1 > > epsilon-r= 1 > > epsilon-rf = 0 > > vdw-type = Cut-off > > ;vdw-modifier = Potential-shift-Verlet > > rvdw-switch = 0 > > rvdw = 1 > > DispCorr = No > > table-extension = 1 > > energygrp-table = > > fourierspacing = 0.12 > > fourier-nx = 0 > > fourier-ny = 0 > > fourier-nz = 0 > > pme-order= 6 > > ewald-rtol = 1e-05 > > ewald-geometry = 3d > > epsilon-surface = 0 > > optimize-fft = yes > > implicit-solvent = No > > gb-algorithm = Still > > nstgbradii = 1 > > rgbradii = 1 > > gb-epsilon-solvent = 80 > > gb-saltconc = 0 > > gb-obc-alpha = 1 > > gb-obc-beta = 0.8 > > gb-obc-gamma = 4.85 > > gb-dielectric-offset = 0.009 > > sa-algorithm = Ace-approximation > > sa-surface-tension = -1 > > tcoupl = v-rescale > > nsttcouple = -1 > > nh-chain-length = 10 > > ;print-nose-hoover-chain-variables = no > > tc-grps = system > > tau-t= 0.1 > > ref-t= 280.00 > > pcoupl = No > > pcoupltype = Isotropic > > nstpcouple = -1 > > tau-p= 1 > > compressibility = > > ref-p= > > refcoord-scaling = No > > > > QMMM = no > > QMMM-grps= > > QMmethod = > > QMMMscheme = normal > > QMbasis = > > QMcharge = > > QMmult = > > SH = > > CASorbitals = > > CASelectrons = > > SAon = > > SAoff= > > SAsteps = > > MMChargeScaleFactor = 1 > > bOPT = > > bTS = > > annealing= > > annealing-npoints= > > annealing-time = > > annealing-temp = > > gen-vel = yes > > gen-temp = 28
[gmx-users] high-temperature MD
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 a high temperature? Should I run the MD(380K) at NPT ensemble or at NPT ensemble? Best regards, Ouyang -- 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)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
