[gmx-users] A question about simulation system includes more than 100000 atoms using Gromacs
Dear Madam/Sir, I have recently tried to use Gromacs to simulation a biolmoleculal system including more than 10 atoms. As usually, the .gro file just supports the system with atom number up to 9. But there are some publications in which researchers used Gromacs to simulate like ribosom systems, which includes more than 200 atoms. So, could you give some advice on how to do it? Does it need to change the source codes? Thanks, Zhuqing -- 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] A question about simulation system includes more than 100000 atoms using Gromacs
my system includes1,700,000 atoms, and runs well with 5.0.4. Sent from my Huawei Mobile 张竹青 zhuqingzh...@ucas.ac.cn wrote: Dear Madam/Sir, I have recently tried to use Gromacs to simulation a biolmoleculal system including more than 10 atoms. As usually, the .gro file just supports the system with atom number up to 9. But there are some publications in which researchers used Gromacs to simulate like ribosom systems, which includes more than 200 atoms. So, could you give some advice on how to do it? Does it need to change the source codes? Thanks, Zhuqing -- 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] A question about simulation system includes more than 100000 atoms using Gromacs
Hi Zhuquing, as far as I know, atom numbers in .gro file are irrelevant - gromacs asigns indices based on the order of records in the file. I my configurations numbers are often quite random, as I copy and paste coordinates from different sources. It never caused any problems in gromacs (neverheless, it can cause troubles in visualisation software). Regards, Jan 2015-07-19 12:10 GMT+02:00 张竹青 zhuqingzh...@ucas.ac.cn: Dear Madam/Sir, I have recently tried to use Gromacs to simulation a biolmoleculal system including more than 10 atoms. As usually, the .gro file just supports the system with atom number up to 9. But there are some publications in which researchers used Gromacs to simulate like ribosom systems, which includes more than 200 atoms. So, could you give some advice on how to do it? Does it need to change the source codes? Thanks, Zhuqing -- 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] Calculating hydrogen bonding density - issues with g_sas?
Hi, and sorry for a bit late reply. g_sas (or gmx sasa) does not compute the volume correctly if your solute crosses a periodic boundary. In 5.1, there is a note to this effect in the documentation, but it is tricky to actually detect this condition in the code. But what this means is that you cannot compute the volume of, e.g., a periodic slab using g_sas. With proper use of trjconv, you can still compute the volume of a multi-molecule droplet. Best regards, Teemu On Wed, Jul 8, 2015 at 6:59 PM Dan Gil dan.gil9...@gmail.com wrote: Is g_sas applicable to more than one molecule at a time? I have 4500 water molecules in the liquid state. I am using the command: g_sas -f traj.trr -s topol.tpr -tv volume.xvg On Tue, Jul 7, 2015 at 10:31 AM, Dan Gil dan.gil9...@gmail.com wrote: I am using the default radius of 0.14 nm. In this case, I believe that it is consistent. Nevertheless, I have tried using a probe much larger with no significant difference in the results. The way I am using g_sas is: I have 4500 water molecules. I specified that I want the volume of all of them. On Tue, Jul 7, 2015 at 10:11 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Is the radius being used consistent with your assumption? Mark On Tue, Jul 7, 2015 at 3:58 PM Dan Gil dan.gil9...@gmail.com wrote: Hi, I am using g_hbond to count the number of h-bonds and then g_sas to calculate the volume. I want to get the number of hydrogen bonds per volume. But I am having issues with g_sas - the volume calculated is about one half of the expected value. For instance, in a pure water system (NVT, SPCE, T=300K) periodic in the x and y directions, volume was found to be about 60nm^3, whereas I expected 130nm^3. I would appreciate any advice! -- 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] RDF
Search for my papers Vitaly V. Chaban. You will find many papers determining solvation/solubility, where it is described how solubility can be obtained from atomistic simulations. RDF alone is not a proper descriptor. However, if you plot COM-COM RDF for C60, you will get some solubility related information (but not numerical solubility). In my personal opinion, even with what you call binders solubility of C60 is water is small. You will not be able to record it using small MD systems. Best of luck. On Sat, Jul 18, 2015 at 7:08 AM, soumadwip ghosh soumadwipgh...@gmail.com wrote: Dear all, I have attempted to show the dynamics of a C60 molecule in presence of aqueous soluble binders. I am using GROMOS53A6 force field and SPC/E water. I took the pdb as well as the itp file of both from the ATB server. I ran simulations using GROMACS 4.5.6 of fullerene both in presence and absence of the organic binders for 70 ns. In order to see whether fullerene becomes water dispersible or not I have planned to to calculate delta G solvation for both the cases using the thermodynamic integration method. But as of now, if in presence of a binder fullerene is more water soluble as compared to its pristine form this should be reflected in the RDF calculation between fullerene center of mass and Oxygen atoms fro water but as you can show in the link below, the reverse thing is happening. Link https://drive.google.com/file/d/0B7SBnQ5YXQSLVFY0MEItUTAzY1E/view?usp=sharing Is there something wrong with my approach. FYI I took 8 SDS binders which wraps around the fullerene molecule. I think I am missing out something very trivial. Any kind of help will be appreciated. Soumadwip Ghosh Research Fellow IITB India -- 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.
[gmx-users] Questions about GROMACS capabilities
Hello GROMACS users, I have a few questions about what is possible in GROMACS: 1.) Is it possible reset the velocity of a subset of molecules in a MD simulation to an arbitrary, non-thermal distribution? I am particularly interested in the situation where all molecules of a certain type are reset to a fixed COM speed in a fixed direction. 2.) If it is possible to reset the velocity of particles in a MD simulation, is it possible to do so with a spatial trigger (e.g., all molecules that reach the top of the unit cell have their velocity reset to a specific speed and direction)? 3.) Is it possible to make a gas-liquid system where there are gas-liquid interactions but no gas-gas interactions? Best, Eric -- 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] segmentation fault
Hi, I am trying to simulate a confined water system with gromacs 5.0.5, however, I am getting the segmentation fault. Below are the gdb backtrace and the build info. Thanks, Sikandar backtrace:: #0 0x7767d8dd in _mm_loadu_pd (tab_coul_F=0x7fffe6217100, tab_coul_V=0x7fffe621b560, ti_S=..., ti=0x0, ctab0_S=0x7fffea947560, ctab1_S=0x7fffea947550, ctabv_S=0x7fffea947510) at /usr/local/gcc-4.7.1/lib/gcc/x86_64-unknown-linux-gnu/4.7.1/include/emmintrin.h:113 #1 load_table_f_v (tab_coul_F=0x7fffe6217100, tab_coul_V=0x7fffe621b560, ti_S=..., ti=0x0, ctab0_S=0x7fffea947560, ctab1_S=0x7fffea947550, ctabv_S=0x7fffea947510) at /home/mashaya1/Apps/gromacs/source/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/../nbnxn_kernel_simd_utils_x86_128d.h:168 #2 0x77688e9b in nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn (nbl=0x7fffe5800920, nbat=0x7fffe6200a80, ic=0x7fffe6205f80, shift_vec=0x7a7de0, f=0x7fffdde37010, fshift=0x7fffe6203740, Vvdw=0x7fffe6203be0, Vc=0x7fffe6203c70) at /home/mashaya1/Apps/gromacs/source/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h:628 #3 0x777c760f in nbnxn_kernel_simd_4xn._omp_fn.0 () at /home/mashaya1/Apps/gromacs/source/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c:412 #4 0x7304681a in gomp_thread_start (xdata=Unhandled dwarf expression opcode 0xf3 ) at ../../../src/gcc-4.7.1/libgomp/team.c:116 #5 0x72c139d1 in start_thread () from /lib64/libpthread.so.0 #6 0x729608fd in clone () from /lib64/libc.so.6 Version and built info. Gromacs version:VERSION 5.0.5-20150513-33467fd GIT SHA1 hash: 33467fd9bc5f94d704b071f0193da0a6ff0ea19b Precision: double Memory model: 64 bit MPI library:MPI OpenMP support: enabled GPU support:disabled invsqrt routine:gmx_software_invsqrt(x) SIMD instructions: SSE4.1 FFT library:fftw-3.3.3-sse2 RDTSCP usage: enabled C++11 compilation: enabled TNG support:enabled Tracing support:disabled Built on: Sun Jul 19 19:24:25 CDT 2015 Built by: mashaya1@taub189 [CMAKE] Build OS/arch: Linux 2.6.32-504.16.2.el6.x86_64 x86_64 Build CPU vendor: GenuineIntel Build CPU brand:Intel(R) Xeon(R) CPU X5650 @ 2.67GHz Build CPU family: 6 Model: 44 Stepping: 2 Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 C compiler: /usr/local/mpi/openmpi-1.6.5-gcc-4.7.1/bin/mpicc GNU 4.7.1 C compiler flags:-msse4.1-Wno-maybe-uninitialized -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -g -fno-inline C++ compiler: /usr/local/mpi/openmpi-1.6.5-gcc-4.7.1/bin/mpicxx GNU 4.7.1 C++ compiler flags: -msse4.1 -std=c++0x -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -g -fno-inline Boost version: 1.51.0 (external) -- 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] How to calculate magnesium (MG) parameters for gbsa.itp
Dear Gromacs Users, I have taken error below after runnig: gmx grompp -f md-implicit-gpu.mdp -c conf.gro -p topol.top -n index.ndx -o md-implicit.tpr GB parameter(s) missing or negative for atom type 'MG' ... Fatal error: Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 1 atomtypes or they might be negative. How can I calculate Magnesium (MG) parameters for gbsa.itp in implicit simulation? I would greatly appreciate if anyone could kindly help me. Best Wishes Hassan -- 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] A question about simulation system includes more than 100000 atoms using Gromacs
Hi Jan, Thank you very much for your reply. I tried to use pdb2gmx (gromacs v4.5.5), in fact, for the chain with the atom number serial larger than 1 in pdb file, it can bot be recognized. Best, Zhuqing -原始邮件- 发件人: Jan Jirsák janjir...@gmail.com 发送时间: 2015年7月19日 星期日 收件人: gmx-us...@gromacs.org 抄送: 主题: Re: [gmx-users] A question about simulation system includes more than 10 atoms using Gromacs Hi Zhuquing, as far as I know, atom numbers in .gro file are irrelevant - gromacs asigns indices based on the order of records in the file. I my configurations numbers are often quite random, as I copy and paste coordinates from different sources. It never caused any problems in gromacs (neverheless, it can cause troubles in visualisation software). Regards, Jan 2015-07-19 12:10 GMT+02:00 张竹青 zhuqingzh...@ucas.ac.cn: Dear Madam/Sir, I have recently tried to use Gromacs to simulation a biolmoleculal system including more than 10 atoms. As usually, the .gro file just supports the system with atom number up to 9. But there are some publications in which researchers used Gromacs to simulate like ribosom systems, which includes more than 200 atoms. So, could you give some advice on how to do it? Does it need to change the source codes? Thanks, Zhuqing -- 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. -- 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] MD exit condition
Hello Gromacs users, In response to a question on setting a group-group distance as an MD exit condition, Mark Abraham suggested that it might be possible to use a table-specified bond that would terminate a simulation by generating an infinite force and crashing mdrun. I am interested in revisiting this idea with a slightly more complex exit condition. How would I define a simulation that will crash when the z-component of a fictious bond between two groups exceeds a certain value in a specific cartesian direction (e.g., the z-component)? Is this impossible in GROMACS? Best, Eric On Thu, Aug 28, 2014 at 6:58 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Thu, Aug 28, 2014 at 3:32 PM, Eric Smoll ericsm...@gmail.com wrote: Hello Gromacs users, I am using Gromacs 4.6.5 Is there a way to set an exit condition during a simulation? I am interested in terminating dynamics when two groups are separated by a certain distance. No. People want this, but it's never been a priority for someone with the knowledge to implement it. Creative use of a bond with a malware user table could produce infinite forces that will get mdrun to blow up shortly after the condition is reached, but I can't honestly recommend that! :-D One reasonable approach might be to use the pull code to achieve the distance in a controlled way. If it is not possible to set an exit condition, I suspect I can post process the trajectory with trjconv using the -exec flag and/or the -trunc flag: 1.) The manual states that the -exec flag will Execute a command for every output frame with the frame number as argument. What kinds of commands I can pass to this flag? Intended for use with -sep or -split. Command gets passed the number of the file most recently written, and then has to go do its own file parsing. I would rather use g_dist or such. 2.) If the -exec is not useful, I plan to analyse the the output of g_dist to find the the time t when two groups exceed my distance criterion and run trjconv -trunc t to crop the trajectory appropriately. Is there a better way? You could probably use NAMD :-) Mark Best, Eric -- 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. -- 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_hbond : normalization autocorrelation function.
Erik,
I want autocorrelation function without normalization.
Exact value at t=0, t=1 is with normalization.
Nilesh
Hi Nilesh,
Iâm not sure what you mean. Both Ac_finSys and Ac are 1 at t=0. What
normalisation do you expect?
Kind regards,
Erik
Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College
Department of Chemistry
Physical Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ
On 19 Jul 2015, at 04:07, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
Hello,
I am calculating autocorrelation function without normalization using
g_hbond
g_hbond -f test.pdb -s 3.tpr -nonormalize -n hydrogen_1.ndx -ac
./test/hbac_3.xvg -num ./test/num_3.xvg
The output, hbac_3.xvg, don't have normalized auto correlation
function.
Here is initial part
@title Hydrogen Bond Autocorrelation
@xaxis label Time (ps)
@yaxis label C(t)
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend Ac\sfin sys\v{}\z{}(t)
@ s1 legend Ac(t)
@ s2 legend Cc\scontact,hb\v{}\z{}(t)
@ s3 legend -dAc\sfs\v{}\z{}/dt
0 1 1 6.67572e-060.761129
0.050.9619280.99214633980.401535
0.10.9598460.9917173496 0.0419408
0.150.9577340.9912813599 0.0340092
0.20.9564460.99101536600.022918
Why is it not normalized ?
Thanks,
Nilesh
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Re: [gmx-users] Problem running equilibration step
Thank you Justin ! -Priyanka On Thu, Jul 16, 2015 at 5:21 PM, Justin Lemkul jalem...@vt.edu wrote: On 7/16/15 7:35 AM, Priyanka Patel wrote: Hello Felipe, Thanks for quick response, I have change my nvt.mdp file according to your instruction, but still getting the following error; Fatal error: Invalid T coupling input: 1 groups, 2 ref-t values and 2 tau-t values Again, the error is rather obvious. You have one group and you're trying to set up two thermostat reference and relaxation values. Also note that you should not use the tutorial's settings (which are for OPLS) when using the CHARMM force field. Those settings are at http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM -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. -- Regards, Priyanka Patel Mo:+91-8805811500 -- 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_hbond : normalization autocorrelation function.
Hi Nilesh,
I’m not sure what you mean. Both Ac_finSys and Ac are 1 at t=0. What
normalisation do you expect?
Kind regards,
Erik
Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College
Department of Chemistry
Physical Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ
On 19 Jul 2015, at 04:07, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote:
Hello,
I am calculating autocorrelation function without normalization using g_hbond
g_hbond -f test.pdb -s 3.tpr -nonormalize -n hydrogen_1.ndx -ac
./test/hbac_3.xvg -num ./test/num_3.xvg
The output, hbac_3.xvg, don't have normalized auto correlation function.
Here is initial part
@title Hydrogen Bond Autocorrelation
@xaxis label Time (ps)
@yaxis label C(t)
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend Ac\sfin sys\v{}\z{}(t)
@ s1 legend Ac(t)
@ s2 legend Cc\scontact,hb\v{}\z{}(t)
@ s3 legend -dAc\sfs\v{}\z{}/dt
0 1 1 6.67572e-060.761129
0.050.9619280.99214633980.401535
0.10.9598460.9917173496 0.0419408
0.150.9577340.9912813599 0.0340092
0.20.9564460.99101536600.022918
Why is it not normalized ?
Thanks,
Nilesh
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