RE: [gmx-users] Overflow problem with test-particle insertion
Hi, This is an interesting issue. The chance is quite small that this happens, but maybe not negligible. In single precision the maximum a float can store is 2^127. This gives a minimum distance of (2^127)^-1/12 = 6.5e-4 nm. The chance of inserting a particle within this radius is dens*3e-10, where dens is the number of particles per nm^3. A typical density of LJ particles is 30 per nm^3, which leads to a chance of 1e-8. Such insertion numbers can be reached, so we probably have to worry about this. However, in your example the distance seems to be around 4e-3, which would give r^-12 = 6e28. This still fits in a float and should not cause problems. So we should make sure we understand what's going on here. Could you file a bugzilla with the files to reproduce this and which insertion is the problematic one? I so two possible solutions: Force tabulated potentials with TPI, this can currently be achieved by setting the environment variable GMX_FORCE_TABLES Or require double precision. But I think both solutions would lead to about 40% lower performance. Berk Date: Wed, 8 Sep 2010 21:16:46 -0400 From: kd...@princeton.edu To: gmx-users@gromacs.org Subject: [gmx-users] Overflow problem with test-particle insertion Hello Gromacs users, I sent a message to the list in June describing what appeared to be a float overflow issue with the energy calculation for test-particle insertions: http://lists.gromacs.org/pipermail/gmx-users/2010-June/052213.html. I have recently tried the test-particle insertion mode in Gromacs-4.5.1, and it seems the problem is still there. Does anyone know how to work around or fix this problem without using tabulated potentials? -Kevin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: multiplication of lambda constant with LJ potential affecting only solvent.
- Original Message - From: Navjeet Ahalawat Date: Thursday, September 9, 2010 16:56 Subject: [gmx-users] Re: multiplication of lambda constant with LJ potential affecting only solvent. To: gmx-users@gromacs.org > Hi all > > I want to change LJ potential for water only by multiplying a > factor lambda. > Can anybody help me that it affect only water not protein. Energy-group tables are the way to implement this. See manual, and mailing list discussions, particularly from Sai Pooja and I in the last few weeks. Note that they will be significantly slower than normal LJ. If performance is an issue, and water dominates the system, you may wish to change the underlying LJ parameters so that the scaled water-water interactions are calculated without the use of tables, and the "normal" water-protein and protein-protein interactions are done with table lookups. This will make more sense once you've read the manual parts :-) Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] restraining atoms to the plane at the bilayer center: pull code ?
Hmm. I am getting the desired output now, at least as far as the pulled
atoms are concerned, they are all close to the bilayer center (was not so in
a free simulation), and therefore my suspicion is that the code is working.
Just to re-iterate, the atoms to be pulled to the bilayer center were
present at the lipid-water interface in both leaflets.
Here is the (apparently successful) pull code:
; COM PULLING
pull= umbrella
pull_geometry = position
pull_dim= N N Y
pull_start= no
pull_nstxout= 5000
pull_nstfout= 5000
pull_ngroups= 2
pull_group0 = POPC
; global atom number of a POPC atom in the middle of the xy box
pull_pbcatom0 = 3100
pull_group1 = C35TOP
; global atom number of a C35 atom in the middle of the xy box
pull_pbcatom1 = 5467
pull_init1 = 0 0 0.0
pull_rate1 = 0
pull_k1 = 500
pull_vec1 = 0 0 0
pull_group2 = C35BOT
; global atom number of a C35 atom in the middle of the xy box
pull_pbcatom2 = 7755
pull_init2 = 0 0 0.0
pull_rate2 = 0
pull_k2 = 500
pull_vec2 = 0 0 0
##
Here is the output from grompp
Pull group natoms pbc atom distance at start reference at t=0
0 4992 3100
116 5467 0.000 0.000 3.184 0.000 0.000 0.000
216 7755 -0.000 0.000 -3.160 0.000 0.000 0.000
###
The average COM pull En. and potential from the log file after 100 ps.
2.96054e+03
###
And here is the output in the log files, detailing the pulling parameters
pull = umbrella
pull_geometry= position
pull_dim (3):
pull_dim[0]=0
pull_dim[1]=0
pull_dim[2]=1
pull_r1 = 1
pull_r0 = 1.5
pull_constr_tol = 1e-06
pull_nstxout = 5000
pull_nstfout = 5000
pull_ngrp= 2
pull_group 0:
atom (4992):
atom[0,...,4991] = {0,...,4991}
weight: not available
pbcatom = 3099
vec (3):
vec[0]= 0.0e+00
vec[1]= 0.0e+00
vec[2]= 0.0e+00
init (3):
init[0]= 0.0e+00
init[1]= 0.0e+00
init[2]= 0.0e+00
rate = 0
k= 0
kB = 0
pull_group 1:
atom (16):
atom[0]=5026
atom[1]=5114
atom[2]=5202
atom[3]=5290
atom[4]=5378
atom[5]=5466
atom[6]=5554
atom[7]=5642
atom[8]=5730
atom[9]=5818
atom[10]=5906
atom[11]=5994
atom[12]=6082
atom[13]=6169
atom[14]=6258
atom[15]=6346
weight: not available
pbcatom = 5466
vec (3):
vec[0]= 0.0e+00
vec[1]= 0.0e+00
vec[2]= 0.0e+00
init (3):
init[0]= 0.0e+00
init[1]= 0.0e+00
init[2]= 0.0e+00
rate = 0
k= 500
kB = 500
pull_group 2:
atom (16):
atom[0]=6434
atom[1]=6522
atom[2]=6610
atom[3]=6698
atom[4]=6786
atom[5]=6874
atom[6]=6962
atom[7]=7050
atom[8]=7138
atom[9]=7226
atom[10]=7314
atom[11]=7402
atom[12]=7490
atom[13]=7578
atom[14]=7666
atom[15]=7754
weight: not available
pbcatom = 7754
vec (3):
vec[0]= 0.0e+00
vec[1]= 0.0e+00
vec[2]= 0.0e+00
init (3):
init[0]= 0.0e+00
init[1]= 0.0e+00
init[2]= 0.0e+00
rate = 0
k= 500
kB = 500
#
I would want to make sure I am doing this right
Best Wishes
Maria
On Wed, Sep 8, 2010 at 4:09 PM, wrote:
> Maria,
>
> I highly doubt that you are correct. If you want more help, please copy and
> paste your commands and some relevant output back to the list.
>
> Chris.
>
> --original message --
>
> Message: 4
> Date: Wed, 8 Sep 2010 15:07:15 +0200
> From: maria goranovic
> Subject: Re: [gmx-users] restraining atoms to the plane at the bilayer
>center:pull code ?
> To: Discussion list for GROMACS users
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Chris,
>
> Thank you for the code. I did check out pull_pbcatomN, and thank you for
> the
> heads up that it is a global index. I used a central atom in the box for
> each of the two groups as pull_pbcatom.
>
> After using the code below with a rate constant of ~ 5500 for about 100 ps,
> I realized that the atoms in different leaflets were being pulled in the
> same direction. I wanted certain atoms of either leaflet to be restrained
> to the bilayer
[gmx-users] How to select atoms dynamically
Dear Elton, Of course, I happy to discuss some questions about CNT in GROMACS. My Email is zhongjin1...@yahoo.com.cn Zhongjin He -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About implicit water simulations
Dear users, I got a question concerning simulations with implicit solvent. So far it is only possible to use this model when applying a cut-off for the long range electrostatic and vdW interactions which leads to bad energy conservation etc. Will there be an update allowing to use reaction-field for instance or user-defined potentials with implicit solvent models? Best regards, Christian Mücksch -- Christian Mücksch Phone: +49 (0)631 205 4287 Department of Physics Fax: +49 (0)631 205 4965 TU Kaiserslautern Email: mueck...@rhrk.uni-kl.de Erwin Schrödinger Straße 67663 Kaiserslautern Germany -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About implicit water simulations
Hi! This is not something that is planned for the immediate future, as useful as it might be. However, for small to medium sized systems one can get good performance by using the all-vs-all kernels. Then the problem of poor energy conservation disappears. Cheers /Per Skickat från min iPhone 9 sep 2010 kl. 15:54 skrev Christian Mücksch : > Dear users, > > I got a question concerning simulations with implicit solvent. So far it is > only possible to use this model when applying a cut-off for the long range > electrostatic and vdW interactions which leads to bad energy conservation etc. > > Will there be an update allowing to use reaction-field for instance or > user-defined potentials with implicit solvent models? > > Best regards, > Christian Mücksch > > -- > Christian Mücksch Phone: +49 (0)631 205 4287 > Department of Physics Fax: +49 (0)631 205 4965 > TU Kaiserslautern Email: mueck...@rhrk.uni-kl.de > Erwin Schrödinger Straße > 67663 Kaiserslautern > Germany > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Overflow problem with test-particle insertion
Hi, I realized now that this is an SSE issue. Normally you would get NAN (or is it INF?). That is treated correctly in the GROMACS TPI code. But in SSE a float "wraps around" when it overflows, which could, in very few cases, lead to a reasonably looking energy value (I check for very high and very low values). I found that you can check for overflows in SSE and committed a fix for 4.5.2. I also filled the first 10 points (up to r=0.02 nm) of the potential/force tables, these used to be zero. These values are only relevant for energy minimization or TPI with extreme atomic overlap. Berk From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] Overflow problem with test-particle insertion Date: Thu, 9 Sep 2010 09:39:42 +0200 Hi, This is an interesting issue. The chance is quite small that this happens, but maybe not negligible. In single precision the maximum a float can store is 2^127. This gives a minimum distance of (2^127)^-1/12 = 6.5e-4 nm. The chance of inserting a particle within this radius is dens*3e-10, where dens is the number of particles per nm^3. A typical density of LJ particles is 30 per nm^3, which leads to a chance of 1e-8. Such insertion numbers can be reached, so we probably have to worry about this. However, in your example the distance seems to be around 4e-3, which would give r^-12 = 6e28. This still fits in a float and should not cause problems. So we should make sure we understand what's going on here. Could you file a bugzilla with the files to reproduce this and which insertion is the problematic one? I so two possible solutions: Force tabulated potentials with TPI, this can currently be achieved by setting the environment variable GMX_FORCE_TABLES Or require double precision. But I think both solutions would lead to about 40% lower performance. Berk Date: Wed, 8 Sep 2010 21:16:46 -0400 From: kd...@princeton.edu To: gmx-users@gromacs.org Subject: [gmx-users] Overflow problem with test-particle insertion Hello Gromacs users, I sent a message to the list in June describing what appeared to be a float overflow issue with the energy calculation for test-particle insertions: http://lists.gromacs.org/pipermail/gmx-users/2010-June/052213.html. I have recently tried the test-particle insertion mode in Gromacs-4.5.1, and it seems the problem is still there. Does anyone know how to work around or fix this problem without using tabulated potentials? -Kevin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] selected forces
Dear Gromacs Users, I've read through various posts on a related issue but am hoping that someone will have some ideas on this or at least point me in the right direction. I am also hoping that some discussion on this will help develop some routines that would allow users to approach this problem as a black box: The system I intend to simulate consists of a polymer surrounded by water, lets call them as energygroups Protein and SOL. At each time step during a molecular dynamics simulation, I need (or would like to) have access to the force on each solvent atom exerted only by the protein atoms and not the other solvent atoms. For now lets assume that the protein is uncharged and so only interacts with the solvent via LJ interactions. I've been ploughing through the code and have gotten to the following: 1) do_force(f) has a force vector array f that is invoked in md.c 2) do_force(f) in sim_util.c calls do_force_lowlevel(f) to determine the bonded and non-bonded interactions. 3) do_force_lowlevel(f) in force.f calls do_nonbonded(f) which I assume will determine the LJ interactions for all particles. 4) do_nonbonded(f) in nonbonded.c seems to have different kernel routines for water and other atoms (as the manual states, forces on water molecules are determined with special kernel loops) 5) do_nonbonded(f) calls a specific nonbonded kernel function and this is where its getting a bit tricky. Any help would be appreciated. I'd like to access the solvent atoms and sum up the forces coming from just the protein/polymer and not the other solvent atoms. Unfortunately doing a mdrun -rerun zeroing out different parts of the hamiltonian is not possible for me because I need the 'selected forces' on the fly and not at the end of the simulation. Any ideas/pointers/help would be greatly appreciated. Thanks in advance. Ali Hassanali -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] pdb2gmx gmx 4.5: issues with atom name in last column
Hi there, when using for example: pdb2gmx -f aQQQ.pdb -o agQQQ.pdb -p agQQQ.top -ff amber99sb -water none I got in the agQQQ.pdb, things like: ATOM 15 NE2 NGL 1 4.309 7.159 2.648 1.00 0.00 N ATOM 16 1HE2 NGL 1 4.030 7.698 3.448 1.00 0.00 HE ATOM 17 2HE2 NGL 1 5.066 7.449 2.048 1.00 0.00 HE ATOM 18 C NGL 1 5.487 2.636 0.037 1.00 0.00 C Notice the last column, in special the "HE". This is wrong! For most programmes it's not a issue since they seem to ignore the last column but this column exist and has a propose. And there programmes that observe this column, like openbabel. If converting this pdb to mol2 I got wrong structure since babel thinks I am dealing with Helium atoms. In gmx 4.0.x the last column was never printed so never had this problem before. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: reg Mopac gromacs compilation problem
Hello, vidhya sankar - If the env. var's are really set and operate correctly, one should look for the problem in the MOPAC library itself. Do you use precompiled libmopac.a or compile it by hand? BTW, did you try to exactly follow the procedure described on my website, from the very beginning?? Best. -- Dr. Vitaly V. Chaban Department of Chemistry University of Rochester Rochester, NY 14642 On Thu, Sep 9, 2010 at 2:18 AM, vidhya sankar wrote: > I am using the following environmental variable > > export LDFLAGS="-L/usr/local/lib -Wl,--wrap,__ctype_b" > export CPPFLAGS=-DUSE_MOPAC > export LIBS="-lmopac -ltest" > then i have typed the following command > > ./configure --with-qmmm-mopac > make > make install > > > --- On *Wed, 8/9/10, Vitaly Chaban * wrote: > > > From: Vitaly Chaban > Subject: Re: reg Mopac gromacs compilation problem > To: scvsankar_...@yahoo.com > Date: Wednesday, 8 September, 2010, 5:48 PM > > > Which environmental variables did you set? > > > -- > Dr. Vitaly V. Chaban > Department of Chemistry > University of Rochester > Rochester, NY 14642 > > > > On Wed, Sep 8, 2010 at 1:27 AM, > http://in.mc955.mail.yahoo.com/mc/compose?to=scvsankar_...@yahoo.com>> > wrote: > > Hello, > > > > Form name: Contacts > > > > > > Message text: > > - > > Dear chaban sir, > > thanks in advance > > When i type the following command in gromacs directory > > ./configure --with-qmmm-mopac --disable-float > > it configure successfully > > but when i compile by make command i got the following error at the end > of my compilation > > > > libs/libgmxpreprocess_d.a ../mdlib/.libs/libmd_d.a > /root/gromacs-4.0.5/src/gmxlib/.libs/libgmx_d.a ../gmxlib/.libs/libgmx_d.a > -lnsl -lfftw3 -lm -lmopac -ltest > > ../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac_SH': > > qm_mopac.c:(.text+0x2a7): undefined reference to `domop_' > > ../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `call_mopac': > > qm_mopac.c:(.text+0x70b): undefined reference to `domop_' > > ../mdlib/.libs/libmd_d.a(qm_mopac.o): In function `init_mopac': > > qm_mopac.c:(.text+0x964): undefined reference to `domldt_' > > collect2: ld returned 1 exit status > > make[3]: *** [grompp] Error 1 > > make[3]: Leaving directory `/root/gromacs-4.0.5/src/kernel' > > make[2]: *** [all-recursive] Error 1 > > make[2]: Leaving directory `/root/gromacs-4.0.5/src' > > make[1]: *** [all] Error 2 > > make[1]: Leaving directory `/root/gromacs-4.0.5/src' > > make: *** [all-recursive] Error 1 > > > > What should i do to avoid this error? i am expecting your reply > > also when i use ./configure --without-qmmm-mopac --disable-float it > compiles successfully > > - > > Sender's name: vidhyasankar > > > > > > IP: 220.227.30.57 > > Date: 08.09.2010, 08:27 > > > > > > Best regards. > > > > > > > > > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] mdyn/A to kJ/mol rad2
Hello, I want to convert force constant from mdyn/A to kJ/mol rad2. How to convert mdyn/A to kJ/mol rad2 Thanks NIlesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] res_com in g_rdf
Hi. I am running simulations with DPPC and water molecules. I made groups from a set of atoms from each DPPC molecule (example: Group 1 = C1, C2, C3 Group 2 = C4, C5, C6). I want to calculate the rdf for the center of mass of each group from each DPPC molecule while excluding groups located on the same molecule. I am using the command line: g_rdf -n index -rdf res_com -s full -o rdf08SEPT106.xvg I thought that I would have to edit my topology file to prevent the rdf from including groups on the same molecule, however, after editing my topology file my rdf does not change. By using the res_com option are groups with the same residue number automatically excluded from the rdf calculation? Emily -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pdb2gmx gmx 4.5: issues with atom name in last column
On 2010-09-09 18.37, Alan wrote: Hi there, when using for example: pdb2gmx -f aQQQ.pdb -o agQQQ.pdb -p agQQQ.top -ff amber99sb -water none I got in the agQQQ.pdb, things like: ATOM 15 NE2 NGL 1 4.309 7.159 2.648 1.00 0.00 N ATOM 16 1HE2 NGL 1 4.030 7.698 3.448 1.00 0.00 HE ATOM 17 2HE2 NGL 1 5.066 7.449 2.048 1.00 0.00 HE ATOM 18 C NGL 1 5.487 2.636 0.037 1.00 0.00 C I can not reproduce this. Can you please file a bugzilla and load up the input pdb file? Notice the last column, in special the "HE". This is wrong! For most programmes it's not a issue since they seem to ignore the last column but this column exist and has a propose. And there programmes that observe this column, like openbabel. If converting this pdb to mol2 I got wrong structure since babel thinks I am dealing with Helium atoms. In gmx 4.0.x the last column was never printed so never had this problem before. Thanks, Alan -- Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<< -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Amber force fields giving LINCS errors
First off I am using gromacs 4.5. I will also post all of my files and errors if they help. If I run a protein in GROMOS96 all my md runs complete succesfully. But if I change to any of the AMBER force fields I get LINCS errors in my positional restraint md run. I have tried using shake, 1 fs step sizes, -heavyh, and many more. Does anyone know what is going on here? The reason I want to use AMBER is the fact that I want to run md on the 30s rybosome and amber converts RNA much easier than GROMOS force fields. Thank you in advance, TJ Mustard Email: musta...@onid.orst.edu Cell: 509-879-4173 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] tip5p.itp in Charmm
Hi, I am running charmmm force field (ff) in gmx 4.5 version and just trying on tip5p water model in it. Unfortunately I only find tip5p.gro is in the ff, not tip5p.itp file. Can anyone help me with hints on constructing it? Many thanks, Yao -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Amber force fields giving LINCS errors
TJ Mustard wrote: First off I am using gromacs 4.5. I will also post all of my files and errors if they help. If I run a protein in GROMOS96 all my md runs complete succesfully. But if I change to any of the AMBER force fields I get LINCS errors in my positional restraint md run. I have tried using shake, 1 fs step sizes, -heavyh, and many more. Does anyone know what is going on here? A complete (but not overly lengthy) post will save everyone a lot of time. Based on the information you've provided here, I see now way to diagnose the problem. The most important information to post would be your .mdp file. Certain settings can influence stability. A description of the hardware, compilers used, etc. can also be useful. -Justin The reason I want to use AMBER is the fact that I want to run md on the 30s rybosome and amber converts RNA much easier than GROMOS force fields. Thank you in advance, TJ Mustard Email: musta...@onid.orst.edu Cell: 509-879-4173 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Amber force fields giving LINCS errors
Of course. I am trying to run the ribosome 30s subunit on gromax 4.5. I chose the AMBER force field since it had the least issues with RNA and that made running pdb2gmx much easier. Everything is fine till I run a md. Below I have attached everything I think is informative. I have run a purely protein md with GROMOS96-43a1 and had no problems, but once I try to run this under AMBER03 it fails with LINCS errors. energy minimization mdp file: cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 5000 ; ; Energy minimizing stuff ; emtol = 200 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no Positional restraint mdp file: define = -DPOSRES constraints = all-bonds integrator = md dt = 0.004 ; ps nsteps = 2500 ; total ps = dt*nsteps nstcomm = 1 nstxout = 200 ; output coordinates every ps = dt*nstxout nstvout = 1000 ; output velocities every ps = dt*nstvout nstfout = 0 nstenergy = 10 nstlog = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 0.1 0.1 0.1 tc_grps = protein RNA SOL NA CL ref_t = 310 310 310 310 310 ; Pressure coupling is on pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is on at 310K (core body temp) gen_vel = yes gen_temp = 310.0 gen_seed = 173529 main molecular dynamics mdp file: define = -DPOSRES constraints = all-bonds integrator = md dt = 0.004 ; ps nsteps = 25000 ; total ps = dt*nsteps nstcomm = 1 nstxout = 200 ; output coordinates every ps = dt*nstxout nstvout = 1000 ; output velocities every ps = dt*nstvout nstfout = 0 nstenergy = 10 nstlog = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 0.1 0.1 0.1 tc_grps = protein RNA SOL NA CL ref_t = 310 310 310 310 310 ; Pressure coupling is on pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is on at 310K (core body temp) gen_vel = yes gen_temp = 310.0 gen_seed = 173529 And my script for running the whole process: pdb2gmx -f receptor.pdb -o receptor.gro -p receptor.top editconf -bt cubic -f receptor.gro -o receptor.gro -c -d 1.5 genbox -cp receptor.gro -cs spc216.gro -o receptor_b4ion.gro -p receptor.top grompp -f em.mdp -c receptor_b4ion.gro -p receptor.top -o receptor_b
Re: [gmx-users] Amber force fields giving LINCS errors
My one thought is that it is to large of a system for GROMACS to run it, yet I have run a small protein in GROMOS96-43a1 and it works but not in any of the AMBER force fields. On September 9, 2010 at 9:35 PM TJ Mustard wrote: Of course. I am trying to run the ribosome 30s subunit on gromax 4.5. I chose the AMBER force field since it had the least issues with RNA and that made running pdb2gmx much easier. Everything is fine till I run a md. Below I have attached everything I think is informative. I have run a purely protein md with GROMOS96-43a1 and had no problems, but once I try to run this under AMBER03 it fails with LINCS errors. energy minimization mdp file: cpp = /usr/bin/cpp define = -DFLEX_SPC constraints = none integrator = steep nsteps = 5000 ; ; Energy minimizing stuff ; emtol = 200 emstep = 0.01 nstcomm = 1 ns_type = grid rlist = 1 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen_vel = no Positional restraint mdp file: define = -DPOSRES constraints = all-bonds integrator = md dt = 0.004 ; ps nsteps = 2500 ; total ps = dt*nsteps nstcomm = 1 nstxout = 200 ; output coordinates every ps = dt*nstxout nstvout = 1000 ; output velocities every ps = dt*nstvout nstfout = 0 nstenergy = 10 nstlog = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 0.1 0.1 0.1 tc_grps = protein RNA SOL NA CL ref_t = 310 310 310 310 310 ; Pressure coupling is on pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is on at 310K (core body temp) gen_vel = yes gen_temp = 310.0 gen_seed = 173529 main molecular dynamics mdp file: define = -DPOSRES constraints = all-bonds integrator = md dt = 0.004 ; ps nsteps = 25000 ; total ps = dt*nsteps nstcomm = 1 nstxout = 200 ; output coordinates every ps = dt*nstxout nstvout = 1000 ; output velocities every ps = dt*nstvout nstfout = 0 nstenergy = 10 nstlog = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 0.1 0.1 0.1 tc_grps = protein RNA SOL NA CL ref_t = 310 310 310 310 310 ; Pressure coupling is on pcoupl = berendsen pcoupltype = isotrop
Re: [gmx-users] Overflow problem with test-particle insertion
Hello.
Probably that will not be related with the original problem but that's
something that came to me when reviewing the tpi.c code:
In line 583 (and follow), it is stated:
if (epot != epot || epot*beta < bU_neg_limit)
{
if (debug)
{
fprintf(debug,"\n time %.3f, step %d:
non-finite energy %f, using exp(-bU)=0\n",t,step,epot);
}
embU = 0;
}
And maybe the condition (after ||) should be:
if (epot != epot || -epot*beta < bU_neg_limit)
Otherwise we could be making a huge number (>exp(50)) equal to 0 instead
of making exp(-50)=0 as intended, isn't it?
Well, I know I could be a bit confused
Javier
El 09/09/10 17:19, Berk Hess escribió:
Hi,
I realized now that this is an SSE issue.
Normally you would get NAN (or is it INF?). That is treated correctly
in the GROMACS TPI code.
But in SSE a float "wraps around" when it overflows, which could, in
very few cases, lead to a reasonably
looking energy value (I check for very high and very low values).
I found that you can check for overflows in SSE and committed a fix
for 4.5.2.
I also filled the first 10 points (up to r=0.02 nm) of the
potential/force tables, these used to be zero.
These values are only relevant for energy minimization or TPI with
extreme atomic overlap.
Berk
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Overflow problem with test-particle insertion
Date: Thu, 9 Sep 2010 09:39:42 +0200
Hi,
This is an interesting issue.
The chance is quite small that this happens, but maybe not negligible.
In single precision the maximum a float can store is 2^127.
This gives a minimum distance of (2^127)^-1/12 = 6.5e-4 nm.
The chance of inserting a particle within this radius is dens*3e-10,
where dens is the number of particles per nm^3.
A typical density of LJ particles is 30 per nm^3, which leads to a
chance of 1e-8.
Such insertion numbers can be reached, so we probably have to worry
about this.
However, in your example the distance seems to be around 4e-3, which would
give r^-12 = 6e28. This still fits in a float and should not cause
problems.
So we should make sure we understand what's going on here.
Could you file a bugzilla with the files to reproduce this and which
insertion
is the problematic one?
I so two possible solutions:
Force tabulated potentials with TPI, this can currently be achieved by
setting
the environment variable GMX_FORCE_TABLES
Or require double precision.
But I think both solutions would lead to about 40% lower performance.
Berk
Date: Wed, 8 Sep 2010 21:16:46 -0400
From: kd...@princeton.edu
To: gmx-users@gromacs.org
Subject: [gmx-users] Overflow problem with test-particle insertion
Hello Gromacs users,
I sent a message to the list in June describing what appeared to be a
float overflow issue with the energy calculation for test-particle
insertions:
http://lists.gromacs.org/pipermail/gmx-users/2010-June/052213.html.
I have recently tried the test-particle insertion mode in
Gromacs-4.5.1, and it seems the problem is still there. Does anyone
know how to work around or fix this problem without using tabulated
potentials?
-Kevin
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--
Javier CEREZO BASTIDA
Estudiante de Doctorado
-
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434
--
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Re: [gmx-users] Amber force fields giving LINCS errors
TJ Mustard wrote: *Positional restraint mdp file:* define = -DPOSRES constraints = all-bonds integrator = md dt = 0.004 ; ps Unless you're using virtual sites (which, per your commands below, you are not) this time step is inappropriately large and is a likely source of instability. With plain constraints, 2 fs is more appropriate. nsteps = 2500 ; total ps = dt*nsteps nstcomm = 1 nstxout = 200 ; output coordinates every ps = dt*nstxout nstvout = 1000 ; output velocities every ps = dt*nstvout nstfout = 0 nstenergy = 10 nstlog = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb= 0.9 rvdw= 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temperature coupling is on Tcoupl = v-rescale tau_t = 0.1 0.1 0.1 0.1 0.1 tc_grps = protein RNA SOL NACL Also a major concern - never couple solvent and ions separately! See here: http://www.gromacs.org/Documentation/Terminology/Thermostats ref_t = 310 310 310 310 310 ; Pressure coupling is on pcoupl = berendsen pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is on at 310K (core body temp) gen_vel = yes gen_temp= 310.0 gen_seed= 173529 *main molecular dynamics mdp file:* define = -DPOSRES Restraints during data collection, or did you paste the wrong file? ; Generate velocities is on at 310K (core body temp) gen_vel = yes Re-generating velocities after equilibration defeats the whole purpose of equilibrating. Per your commands below, you are not preserving the velocities (grompp -t with .trr or .cpt file) obtained during your PR equilibration. gen_temp= 310.0 gen_seed= 173529 *And my script for running the whole process:* pdb2gmx -f receptor.pdb -o receptor.gro -p receptor.top editconf -bt cubic -f receptor.gro -o receptor.gro -c -d 1.5 genbox -cp receptor.gro -cs spc216.gro -o receptor_b4ion.gro -p receptor.top grompp -f em.mdp -c receptor_b4ion.gro -p receptor.top -o receptor_b4ion.tpr genion -s receptor_b4ion.tpr -o receptor_b4em.gro -neutral -conc 0.0001 -pname NA -nname CL -g receptor_ion.log -p receptor.top *Here I select the SOL for ions...* grompp -f em.mdp -c receptor_b4em.gro -p receptor.top -o receptor_em.tpr mdrun -v -s receptor_em.tpr -c "$base"_after_em.gro -g emlog.log grompp -f pr.mdp -c receptor_after_em.gro -p receptor.top -o receptor_pr.tpr mdrun -v -s receptor_pr.tpr -o receptor_pr.trr -e pr.edr -c receptor_after_pr.gro -g prlog.log -cpi state_pr.cpt -cpo state_pr.cpt grompp -f md.mdp -c receptor_after_pr.gro -p receptor.top -o receptor_md.tpr mdrun -s receptor_md.tpr -o receptor_md.trr -c receptor_after_pr.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt *Where receptor is of course my protein/RNA pdb name* I always make sure that the pdb doesn't give me notes or warnings or errors of course in the pdb2gmx step. Most of the time I minimize to my computers "machine precision." ** *This is the return I get from the "EM" step:* Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 200 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) writing lowest energy coordinates. Steepest Descents converged to machine precision in 324 steps, but did not reach the requested Fmax < 200. Potential Energy = -1.986e+07 Maximum force = 8.7276396e+03 on atom 19080 This is a very high Fmax, indicating that you have bad clashes in your system that, when combined with the parameters above, surely leads to an unstable system. The fact that Gromos96 works is a bit curious, but you have too many potential pitfalls listed here to specifically diagnose the difference based on this information alone. -Justin Norm of force = 3.8592850e+01 *I will get this error sometime in the "PR" step of my script:* step 0 Step 11 Warning: pressure scaling more than 1%, mu: 1.03087 1.03087 1.03087 Step 11 Warning: pressure scaling more than 1%, mu: 1.03087 1.03087 1.03087 Step 21 Warning: pressure scaling more than 1%, mu: 0.849053 0.849053 0.849053 Step 21 Warning:
Re: [gmx-users] mdyn/A to kJ/mol rad2
- Original Message - From: Nilesh Dhumal Date: Friday, September 10, 2010 4:41 Subject: [gmx-users] mdyn/A to kJ/mol rad2 To: gmx-users@gromacs.org > Hello, > I want to convert force constant from mdyn/A to kJ/mol rad2. > How to convert mdyn/A to kJ/mol rad2 So what's the definition of a dyne? Mark > Thanks > > NIlesh > > > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Amber force fields giving LINCS errors
On September 9, 2010 at 10:04 PM "Justin A. Lemkul" wrote: > > > TJ Mustard wrote: > > > > > *Positional restraint mdp file:* > > > > > > > > define = -DPOSRES > > constraints = all-bonds > > integrator = md > > dt = 0.004 ; ps > > Unless you're using virtual sites (which, per your commands below, you are not) > this time step is inappropriately large and is a likely source of instability. > With plain constraints, 2 fs is more appropriate. Yes I usually run at 2 fs. I was actually running a huge batch of these at varying time steps and with or without -heavyh. > > > nsteps = 2500 ; total ps = dt*nsteps > > nstcomm = 1 > > nstxout = 200 ; output coordinates every ps = dt*nstxout > > nstvout = 1000 ; output velocities every ps = dt*nstvout > > nstfout = 0 > > nstenergy = 10 > > nstlog = 10 > > nstlist = 10 > > ns_type = grid > > rlist = 0.9 > > coulombtype = PME > > rcoulomb = 0.9 > > rvdw = 1.0 > > fourierspacing = 0.12 > > fourier_nx = 0 > > fourier_ny = 0 > > fourier_nz = 0 > > pme_order = 6 > > ewald_rtol = 1e-5 > > optimize_fft = yes > > ; Berendsen temperature coupling is on > > Tcoupl = v-rescale > > tau_t = 0.1 0.1 0.1 0.1 0.1 > > tc_grps = protein RNA SOL NA CL > > Also a major concern - never couple solvent and ions separately! See here: > > http://www.gromacs.org/Documentation/Terminology/Thermostats > Yes I have since switched to a Protein Non-protein setting. > > ref_t = 310 310 310 310 310 > > ; Pressure coupling is on > > pcoupl = berendsen > > pcoupltype = isotropic > > tau_p = 0.5 > > compressibility = 4.5e-5 > > ref_p = 1.0 > > ; Generate velocities is on at 310K (core body temp) > > gen_vel = yes > > gen_temp = 310.0 > > gen_seed = 173529 > > > > > > > > > > > > *main molecular dynamics mdp file:* > > > > > > > > > > > define = -DPOSRES > > Restraints during data collection, or did you paste the wrong file? Yeah that will be fixed asap. > > > > > ; Generate velocities is on at 310K (core body temp) > > gen_vel = yes > > Re-generating velocities after equilibration defeats the whole purpose of > equilibrating. Per your commands below, you are not preserving the velocities > (grompp -t with .trr or .cpt file) obtained during your PR equilibration. > Yeah that will be fixed asap. > > gen_temp = 310.0 > > gen_seed = 173529 > > > > > > > > > > > > *And my script for running the whole process:* > > > > > > > > pdb2gmx -f receptor.pdb -o receptor.gro -p receptor.top > > > > editconf -bt cubic -f receptor.gro -o receptor.gro -c -d 1.5 > > > > genbox -cp receptor.gro -cs spc216.gro -o receptor_b4ion.gro -p receptor.top > > > > grompp -f em.mdp -c receptor_b4ion.gro -p receptor.top -o receptor_b4ion.tpr > > > > genion -s receptor_b4ion.tpr -o receptor_b4em.gro -neutral -conc 0.0001 > > -pname NA -nname CL -g receptor_ion.log -p receptor.top > > > > > > > > *Here I select the SOL for ions...* > > > > > > > > grompp -f em.mdp -c receptor_b4em.gro -p receptor.top -o receptor_em.tpr > > > > mdrun -v -s receptor_em.tpr -c "$base"_after_em.gro -g emlog.log > > > > grompp -f pr.mdp -c receptor_after_em.gro -p receptor.top -o receptor_pr.tpr > > > > mdrun -v -s receptor_pr.tpr -o receptor_pr.trr -e pr.edr -c > > receptor_after_pr.gro -g prlog.log -cpi state_pr.cpt -cpo state_pr.cpt > > > > grompp -f md.mdp -c receptor_after_pr.gro -p receptor.top -o receptor_md.tpr > > > > mdrun -s receptor_md.tpr -o receptor_md.trr -c receptor_after_pr.gro -g > > md.log -e md.edr -cpi state_md.cpt -cpo state
Re: [gmx-users] GFP Simulation
> Dear Gmxers, > > I am working on a new project and I plan to do some molecular dynamic > simulation on an engineered GFP molecule. I have been searching for the > parameters for the GFP chromophore without success. Could some one help > me? Any > reference or parameters will be appreciated. Nathalie Reuter, Hai Lin,and Walter Thiel Green Fluorescent Proteins: Empirical Force Field for the Neutral and Deprotonated Forms of the Chromophore. Molecular Dynamics Simulations of the Wild Type and S65T Mutant > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
RE: [gmx-users] Overflow problem with test-particle insertion
Hi, Thank you for taking the time to fix the issue. I would be very interested in testing out the modified code, but unfortunately I have had some difficulties compiling the Gromacs code obtained straight from GIT. In particular, I encounter the following error: ~/gromacs/src/tools/gmx_membed.c:1095: error: expected declaration specifiers or ‘...’ before ‘gmx_global_stat_t’ If you are curious to see the log and CMake cache files from the build, I have attached them to this email. I could also just patch the relevant parts of version 4.5.1 and test that out. If this would be feasible, then what specific lines should I modify? -Kevin Date: Thu, 9 Sep 2010 17:19:36 +0200 From: Berk Hess Subject: RE: [gmx-users] Overflow problem with test-particle insertion To: Discussion list for GROMACS users Message-ID: Content-Type: text/plain; charset="iso-8859-1" Hi, I realized now that this is an SSE issue. Normally you would get NAN (or is it INF?). That is treated correctly in the GROMACS TPI code. But in SSE a float "wraps around" when it overflows, which could, in very few cases, lead to a reasonably looking energy value (I check for very high and very low values). I found that you can check for overflows in SSE and committed a fix for 4.5.2. I also filled the first 10 points (up to r=0.02 nm) of the potential/force tables, these used to be zero. These values are only relevant for energy minimization or TPI with extreme atomic overlap. Berk From: g...@hotmail.com To: gmx-users@gromacs.org Subject: RE: [gmx-users] Overflow problem with test-particle insertion Date: Thu, 9 Sep 2010 09:39:42 +0200 Hi, This is an interesting issue. The chance is quite small that this happens, but maybe not negligible. In single precision the maximum a float can store is 2^127. This gives a minimum distance of (2^127)^-1/12 = 6.5e-4 nm. The chance of inserting a particle within this radius is dens*3e-10, where dens is the number of particles per nm^3. A typical density of LJ particles is 30 per nm^3, which leads to a chance of 1e-8. Such insertion numbers can be reached, so we probably have to worry about this. However, in your example the distance seems to be around 4e-3, which would give r^-12 = 6e28. This still fits in a float and should not cause problems. So we should make sure we understand what's going on here. Could you file a bugzilla with the files to reproduce this and which insertion is the problematic one? I so two possible solutions: Force tabulated potentials with TPI, this can currently be achieved by setting the environment variable GMX_FORCE_TABLES Or require double precision. But I think both solutions would lead to about 40% lower performance. Berk Date: Wed, 8 Sep 2010 21:16:46 -0400 From: kd...@princeton.edu To: gmx-users@gromacs.org Subject: [gmx-users] Overflow problem with test-particle insertion Hello Gromacs users, I sent a message to the list in June describing what appeared to be a float overflow issue with the energy calculation for test-particle insertions: http://lists.gromacs.org/pipermail/gmx-users/2010-June/052213.html. I have recently tried the test-particle insertion mode in Gromacs-4.5.1, and it seems the problem is still there. Does anyone know how to work around or fix this problem without using tabulated potentials? -Kevin build_output.tar.gz Description: GNU Zip compressed data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] tip5p.itp in Charmm
- Original Message - From: Yao Yao Date: Friday, September 10, 2010 6:05 Subject: [gmx-users] tip5p.itp in Charmm To: gmx-users@gromacs.org > Hi, > > I am running charmmm force field (ff) in gmx 4.5 version and > just trying on tip5p water model in it. Unfortunately I only > find tip5p.gro is in the ff, not tip5p.itp file. Can anyone help > me with hints on constructing it? You can copy the tip5p.itp files from any of the other force fields. I'll fix the error in the development version. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] tip5p.itp in Charmm
- Original Message - From: Mark Abraham Date: Friday, September 10, 2010 8:59 Subject: Re: [gmx-users] tip5p.itp in Charmm To: Discussion list for GROMACS users > > > - Original Message - > From: Yao Yao > Date: Friday, September 10, 2010 6:05 > Subject: [gmx-users] tip5p.itp in Charmm > To: gmx-users@gromacs.org > > > Hi, > > > > I am running charmmm force field (ff) in gmx 4.5 version and > > just trying on tip5p water model in it. Unfortunately I only > > find tip5p.gro is in the ff, not tip5p.itp file. Can anyone help > > me with hints on constructing it? > > You can copy the tip5p.itp files from any of the other force fields. I'll fix > the error in the development version. Actually it's more complex than that. I've made a tip5p.itp plus supporting changes in git release-4-5-patches by analogy with AMBER03's TIP5p and CHARMM's TIP[34]p. You can download and install that (see webpage) and just copy the charmm27.ff directory to your working directory to get access to tip5p, or wait for GROMACS 4.5.2. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Overflow problem with test-particle insertion
Hi, Thank you for taking the time to fix the issue. I would be very interested in testing out the modified code, but unfortunately I have had some difficulties compiling the Gromacs code obtained straight from GIT. In particular, I encounter the following error: ~/gromacs/src/tools/gmx_ membed.c:1095: error: expected declaration specifiers or ‘...’ before ‘gmx_global_stat_t’ If you are curious to see the log and CMake cache files from the build, I have attached them to this email. I could also just patch the relevant parts of version 4.5.1 and test that out. If this would be feasible, then what specific lines should I modify? -Kevin Date: Thu, 9 Sep 2010 17:19:36 +0200 > From: Berk Hess > Subject: RE: [gmx-users] Overflow problem with test-particle insertion > To: Discussion list for GROMACS users > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > > Hi, > > I realized now that this is an SSE issue. > Normally you would get NAN (or is it INF?). That is treated correctly in > the GROMACS TPI code. > But in SSE a float "wraps around" when it overflows, which could, in very > few cases, lead to a reasonably > looking energy value (I check for very high and very low values). > I found that you can check for overflows in SSE and committed a fix for > 4.5.2. > I also filled the first 10 points (up to r=0.02 nm) of the potential/force > tables, these used to be zero. > These values are only relevant for energy minimization or TPI with extreme > atomic overlap. > > Berk > > From: g...@hotmail.com > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] Overflow problem with test-particle insertion > Date: Thu, 9 Sep 2010 09:39:42 +0200 > > > > > > > > > Hi, > > This is an interesting issue. > The chance is quite small that this happens, but maybe not negligible. > In single precision the maximum a float can store is 2^127. > This gives a minimum distance of (2^127)^-1/12 = 6.5e-4 nm. > The chance of inserting a particle within this radius is dens*3e-10, > where dens is the number of particles per nm^3. > A typical density of LJ particles is 30 per nm^3, which leads to a chance > of 1e-8. > Such insertion numbers can be reached, so we probably have to worry about > this. > > However, in your example the distance seems to be around 4e-3, which would > give r^-12 = 6e28. This still fits in a float and should not cause > problems. > So we should make sure we understand what's going on here. > Could you file a bugzilla with the files to reproduce this and which > insertion > is the problematic one? > > I so two possible solutions: > Force tabulated potentials with TPI, this can currently be achieved by > setting > the environment variable GMX_FORCE_TABLES > Or require double precision. > But I think both solutions would lead to about 40% lower performance. > > Berk > > > Date: Wed, 8 Sep 2010 21:16:46 -0400 > From: kd...@princeton.edu > To: gmx-users@gromacs.org > Subject: [gmx-users] Overflow problem with test-particle insertion > > Hello Gromacs users, > > I sent a message to the list in June describing what appeared to be a float > overflow issue with the energy calculation for test-particle insertions: > http://lists.gromacs.org/pipermail/gmx-users/2010-June/052213.html. > > > I have recently tried the test-particle insertion mode in Gromacs-4.5.1, > and it seems the problem is still there. Does anyone know how to work around > or fix this problem without using tabulated potentials? > > -Kevin > > build_output.tar.gz Description: GNU Zip compressed data -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Overflow problem with test-particle insertion
Hi, Thank you for taking the time to fix the issue. I would be very interested in testing out the modified code, but unfortunately I have had some difficulties compiling the Gromacs code obtained straight from GIT. In particular, I encounter the following error: ~/gromacs/src/tools/gmx_membed.c:1095: error: expected declaration specifiers or ‘...’ before ‘gmx_global_stat_t’ If you are curious to see the log and CMake cache files from the build, I sent them in a previous email to the list (though the text of the message somehow got scrubbed). I could also just patch the relevant parts of version 4.5.1 and test that out. If this would be feasible, then what specific lines should I modify? -Kevin > Date: Thu, 9 Sep 2010 17:19:36 +0200 > From: Berk Hess > Subject: RE: [gmx-users] Overflow problem with test-particle insertion > To: Discussion list for GROMACS users > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > > Hi, > > I realized now that this is an SSE issue. > Normally you would get NAN (or is it INF?). That is treated correctly in the > GROMACS TPI code. > But in SSE a float "wraps around" when it overflows, which could, in very few > cases, lead to a reasonably > looking energy value (I check for very high and very low values). > I found that you can check for overflows in SSE and committed a fix for 4.5.2. > I also filled the first 10 points (up to r=0.02 nm) of the potential/force > tables, these used to be zero. > These values are only relevant for energy minimization or TPI with extreme > atomic overlap. > > Berk > > From: g...@hotmail.com > To: gmx-users@gromacs.org > Subject: RE: [gmx-users] Overflow problem with test-particle insertion > Date: Thu, 9 Sep 2010 09:39:42 +0200 > > > > > > > > > Hi, > > This is an interesting issue. > The chance is quite small that this happens, but maybe not negligible. > In single precision the maximum a float can store is 2^127. > This gives a minimum distance of (2^127)^-1/12 = 6.5e-4 nm. > The chance of inserting a particle within this radius is dens*3e-10, > where dens is the number of particles per nm^3. > A typical density of LJ particles is 30 per nm^3, which leads to a chance of > 1e-8. > Such insertion numbers can be reached, so we probably have to worry about > this. > > However, in your example the distance seems to be around 4e-3, which would > give r^-12 = 6e28. This still fits in a float and should not cause problems. > So we should make sure we understand what's going on here. > Could you file a bugzilla with the files to reproduce this and which insertion > is the problematic one? > > I so two possible solutions: > Force tabulated potentials with TPI, this can currently be achieved by setting > the environment variable GMX_FORCE_TABLES > Or require double precision. > But I think both solutions would lead to about 40% lower performance. > > Berk > > > Date: Wed, 8 Sep 2010 21:16:46 -0400 > From: kd...@princeton.edu > To: gmx-users@gromacs.org > Subject: [gmx-users] Overflow problem with test-particle insertion > > Hello Gromacs users, > > I sent a message to the list in June describing what appeared to be a float > overflow issue with the energy calculation for test-particle insertions: > http://lists.gromacs.org/pipermail/gmx-users/2010-June/052213.html. > > > I have recently tried the test-particle insertion mode in Gromacs-4.5.1, and > it seems the problem is still there. Does anyone know how to work around or > fix this problem without using tabulated potentials? > > -Kevin > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] selected forces
- Original Message - From: Ali Hassanali Date: Friday, September 10, 2010 2:21 Subject: [gmx-users] selected forces To: gmx-users@gromacs.org > Dear Gromacs Users, > > I've read through various posts on a related issue but am hoping > that someone will have some ideas on this or at least point me > in the right direction. I am also hoping that some discussion on > this will help develop some routines that would allow users to > approach this problem as a black box: > > The system I intend to simulate consists of a polymer surrounded > by water, lets call them as energygroups Protein and SOL. At > each time step during a molecular dynamics simulation, I need > (or would like to) have access to the force on each solvent atom > exerted only by the protein atoms and not the other solvent > atoms. For now lets assume that the protein is uncharged and so > only interacts with the solvent via LJ interactions. > I've been ploughing through the code and have gotten to the following: > > 1) do_force(f) has a force vector array f that is invoked in md.c > 2) do_force(f) in sim_util.c calls do_force_lowlevel(f) to > determine the bonded and non-bonded interactions. > 3) do_force_lowlevel(f) in force.f calls do_nonbonded(f) which I > assume will determine the LJ interactions for all particles. > 4) do_nonbonded(f) in nonbonded.c seems to have different kernel > routines for water and other atoms (as the manual states, forces > on water molecules are determined with special kernel loops) > 5) do_nonbonded(f) calls a specific nonbonded kernel function > and this is where its getting a bit tricky. Any help would be > appreciated. I'd like to access the solvent atoms and sum up the > forces coming from just the protein/polymer and not the other > solvent atoms. You've certainly done your homework - that's a fairly good picture of how things work. If you define a suitable energy monitor groups (see 3.3 of manual) then GROMACS will calculate energies and forces within and between those groups, e.g. SOL-SOL, SOL-Protein, Protein-Protein. So it occurs to me that what you want to do is arrange the ordering of your groups so that GROMACS computes SOL-Protein first (that might require some coding to reorder the looping - step through with a debugger to see how this is working). Then the contents of the f vector will be the LJ + charge forces that you want, so you just need to interrupt the looping over energy groups at that point and do whatever it is you need to do. (Check that bonded forces haven't been computed yet.) If you really need LJ only, and charges are present in both groups, then you will need to rework the nblist construction so that this pair of groups is sent first to an LJ-only kernel, then to a charge-only kernel, so that you can interrupt when you need to. Whatever you do, don't touch the code inside any kernel or your simulations will still be running when your grandchildren retire :-) Later when you consider charge interactions, be aware that this kind of group-wise decomposition is impossible for the long-range component of PME, if you use that. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] parallel run problem for nwall
Dear Sir, I am using nwall to run my system. My version is Gromacs 4.0.7. Interestingly, I could parallel run my system on 1 node with 4 or 8 cpus, but when I run it on multi-node PC-cluster, it always fails and gives no message at all. I wonder if you could help me to resolve this problem? Thanks a lot! Yi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] parallel run problem for nwall
- Original Message - From: Yi Gao Date: Friday, September 10, 2010 12:23 Subject: [gmx-users] parallel run problem for nwall To: gmx-users@gromacs.org > Dear Sir, > > I am using nwall to run my system. My version is Gromacs > 4.0.7. Interestingly, I could parallel run my system on 1 node with 4 or 8 > cpus, but when I run it on multi-node PC-cluster, it always fails and gives > no message at all. I wonder if you could help me to resolve this problem? > Thanks a lot! First, find out if your MPI is configured to use the multiple nodes, e.g. with a hostfile. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] parallel run problem for nwall
Gromacs is running well on multi-nodes without nwall. But with nwall, it doesn't work. Yi On Thu, Sep 9, 2010 at 9:28 PM, Mark Abraham wrote: > > > - Original Message - > From: Yi Gao > Date: Friday, September 10, 2010 12:23 > Subject: [gmx-users] parallel run problem for nwall > To: gmx-users@gromacs.org > > > Dear Sir, > > > > I am using nwall to run my system. My version is Gromacs 4.0.7. > Interestingly, I could parallel run my system on 1 node with 4 or 8 cpus, > but when I run it on multi-node PC-cluster, it always fails and gives no > message at all. I wonder if you could help me to resolve this problem? > Thanks a lot! > > First, find out if your MPI is configured to use the multiple nodes, e.g. > with a hostfile. > > Mark > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
