[gmx-users] nvt equilibration output
Respected sir, I am studying about micelle formation .. After setting box and adding water i went for energy minimization and then went for nvt equilibration for 1ns. when i visualized my nvt.pdb file, i found that my protein comes together and formed three micelle like structure. but my box got separated. i dono why i got two separate box. can anyone tell me why this occurs.. i tried many times.. but still i am getting the same.. but i already performed dynamics for 30 monomers.. that time it went well.. now i am getting my output like this.. i checked the system temperature.. its in equilibrium at 299.9k. please help me with your answer.. Thanking you. -- 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] nvt equilibration output
On 16/05/2012 4:18 PM, priya thiyagarajan wrote: Respected sir, I am studying about micelle formation .. After setting box and adding water i went for energy minimization and then went for nvt equilibration for 1ns. when i visualized my nvt.pdb file, i found that my protein comes together and formed three micelle like structure. but my box got separated. i dono why i got two separate box. can anyone tell me why this occurs.. i tried many times.. but still i am getting the same.. but i already performed dynamics for 30 monomers.. that time it went well.. now i am getting my output like this.. i checked the system temperature.. its in equilibrium at 299.9k. Whatever you're observing is almost certainly normal, and you need to be sure you understand http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. The advice there, and perhaps further options you can see in trjconv -h will be necessary to manipulate the trajectory so that it looks the way you want it to. 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] nvt equilibration output
Hi Priya, My query is different than your problem .. I wondered Is you use position restrained in nvt...?? In position restrained protein comes togather or you remove position restraind ... Sorry for trouble you... With Best wishes, Rama David -- 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: NVT conserved-energy lysozyme
On 16/05/2012 1:50 AM, daviddesancho wrote: Thanks Florian and Mark for your replies. I have run the simulation for longer (one order of magnitude longer, i.e. 1 ns) and what I get now is that the 'conserved energy' follows its drift linearly. Now, of course, we are speaking about 1.2% drift/ns in the value of the energy, which seems quite substantial. http://gromacs.5086.n6.nabble.com/file/n4981453/equil_nvt.png Second, I have compiled and run with double precision. Although the value for the conserved energy is slightly different, the slope of E vs time is essentially identical. -- View this message in context: http://gromacs.5086.n6.nabble.com/NVT-conserved-energy-lysozyme-tp4980918p4981453.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. What's your full .mdp and GROMACS 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
[gmx-users] DSSP configuration in Gromacs 4.5.5
Dear all, How to install DSSP in Gromacs 4.5.5. i set environmental variable export DSSP=/usr/local/bin/dssp and checked. I have refereed many posts related to dssp issue and tried with new and old dssp executable but confused. While running i got error Segmentation fault. Help me to solve this problem. Thanks in advance. -- -- Regards, N. Sathishkumar, -- 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] DSSP configuration in Gromacs 4.5.5
On 16/05/2012 4:54 PM, Sathish wrote: Dear all, How to install DSSP in Gromacs 4.5.5. i set environmental variable export DSSP=/usr/local/bin/dssp and checked. I have refereed many posts related to dssp issue and tried with new and old dssp executable but confused. While running i got error Segmentation fault. Help me to solve this problem. There's really nothing much that can be said beyond what is in do_dssp -h. If the above environment variable points to a valid old-style DSSP executable (does it? does it run?) then do_dssp should work. 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] Re: NVT conserved-energy lysozyme
Gromacs version is 4.5.5 and mdp file is that from Justin's tutorial, step 6 (http://bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/nvt.mdp) Thanks -David -- View this message in context: http://gromacs.5086.n6.nabble.com/NVT-conserved-energy-lysozyme-tp4980918p4990033.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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] DSSP configuration in Gromacs 4.5.5
Dear Sir, Thank u for reply and the old dssp executable was working fine, [root@localhost]# dssp COPYRIGHT W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995 CMBI version by elmar.krie...@cmbi.ru.nl / April 1, 2010 USAGE dssp [Options] PDB_File DSSP_File - Read PDB_File and write DSSP_File dssp [Options] -- dssp_file - Read from stdin and write DSSP_File dssp -h - Display this help screen OPTIONS -na Disables the calculation of accessible surface. -cClassic (old) format. -wWide 2002 format (for future use,not the current standard). -vVerbose. --Read from standard input. -h -? Prints a help message. -VPrints version, as in first line of the output. ADDITIONAL OPTIONS CONTRIBUTED BY DSSP USERS By emmanuel.cource...@toulouse.inra.fr -ssa Adds information about disulfide bonds to output file -xRenames residues with incomplete sidechains to 'X' -alt2 Keeps an additional AltLoc indicator at the line ends [root@localhost]# and i have checked one again the path of DSSP [root@localhost sathish]# echo $DSSP /usr/local/bin/dssp [root@localhost sathish]# but while running with do_dssp has problem. [root@localhost sathish]# do_dssp -f xxx.xtc -s xxx.tpr -n index.ndx -o ss.xpm :-) G R O M A C S (-: Grunge ROck MAChoS :-) VERSION 4.5.5-dev-20120318-375fa98 (-: . . . Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision) Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision) Segmentation fault (core dumped) [root@localhost sathish]# Am not clear to understand this problem. help me -- -- Regards, N. Sathishkumar, sath...@khu.ac.kr On Wed, May 16, 2012 at 4:02 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 16/05/2012 4:54 PM, Sathish wrote: Dear all, How to install DSSP in Gromacs 4.5.5. i set environmental variable export DSSP=/usr/local/bin/dssp and checked. I have refereed many posts related to dssp issue and tried with new and old dssp executable but confused. While running i got error Segmentation fault. Help me to solve this problem. There's really nothing much that can be said beyond what is in do_dssp -h. If the above environment variable points to a valid old-style DSSP executable (does it? does it run?) then do_dssp should work. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] DSSP configuration in Gromacs 4.5.5
On 16/05/2012 5:33 PM, Sathish wrote: Dear Sir, Thank u for reply and the old dssp executable was working fine, [root@localhost]# dssp COPYRIGHT W. Kabsch, C. Sander and MPI-MF, 1983, 1985, 1988, 1994 1995 CMBI version by elmar.krie...@cmbi.ru.nl mailto:elmar.krie...@cmbi.ru.nl / April 1, 2010 USAGE dssp [Options] PDB_File DSSP_File - Read PDB_File and write DSSP_File dssp [Options] -- dssp_file - Read from stdin and write DSSP_File dssp -h - Display this help screen OPTIONS -na Disables the calculation of accessible surface. -cClassic (old) format. -wWide 2002 format (for future use,not the current standard). -vVerbose. --Read from standard input. -h -? Prints a help message. -VPrints version, as in first line of the output. ADDITIONAL OPTIONS CONTRIBUTED BY DSSP USERS By emmanuel.cource...@toulouse.inra.fr mailto:emmanuel.cource...@toulouse.inra.fr -ssa Adds information about disulfide bonds to output file -xRenames residues with incomplete sidechains to 'X' -alt2 Keeps an additional AltLoc indicator at the line ends [root@localhost]# and i have checked one again the path of DSSP [root@localhost sathish]# echo $DSSP /usr/local/bin/dssp [root@localhost sathish]# but while running with do_dssp has problem. [root@localhost sathish]# do_dssp -f xxx.xtc -s xxx.tpr -n index.ndx -o ss.xpm :-) G R O M A C S (-: Grunge ROck MAChoS :-) VERSION 4.5.5-dev-20120318-375fa98 (-: You are not using 4.5.5. If you'd shown this the first time, you'd have used less of everybody's time. Maybe this version is one that is updated to use the new DSSP. Maybe you should go and use 4.5.5. Also, don't do routine work logged in as root, unless you like reinstalling your whole operating system. Mark . . . Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision) Reading file erbb_md_5.tpr, VERSION 4.5.5-dev-20120318-375fa98 (single precision) Segmentation fault (core dumped) [root@localhost sathish]# Am not clear to understand this problem. help me -- -- Regards, N. Sathishkumar, mailto:sath...@khu.ac.kr On Wed, May 16, 2012 at 4:02 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 16/05/2012 4:54 PM, Sathish wrote: Dear all, How to install DSSP in Gromacs 4.5.5. i set environmental variable export DSSP=/usr/local/bin/dssp and checked. I have refereed many posts related to dssp issue and tried with new and old dssp executable but confused. While running i got error Segmentation fault. Help me to solve this problem. There's really nothing much that can be said beyond what is in do_dssp -h. If the above environment variable points to a valid old-style DSSP executable (does it? does it run?) then do_dssp should work. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-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 mailto: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] pdb2gmx Warning: Long Bond
Hi If I use pdb2gmx -f mymol.pdb -water tip3p (CHARMM27 force field) I got warnings like this: Making bonds... Warning: Long Bond (1-2 = 0.261872 nm) Warning: Long Bond (2-4 = 0.267812 nm) Warning: Long Bond (6-4 = 0.260531 nm) and so on For what problem tries GROMACS to warn me? Should I change something? In my .rtp parametrization file in the CHARMM27 folder I gave the equilibrium bond length in angstrom with corresponding force constant in kcal/mol, that are out of a supporting Information of a group, that made quantum mechanical calculations with my molecule. Thanks for help Greetings -- 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 Warning: Long Bond
On 16/05/2012 5:50 PM, Lara Bunte wrote: Hi If I use pdb2gmx -f mymol.pdb -water tip3p (CHARMM27 force field) I got warnings like this: Making bonds... Warning: Long Bond (1-2 = 0.261872 nm) Warning: Long Bond (2-4 = 0.267812 nm) Warning: Long Bond (6-4 = 0.260531 nm) and so on For what problem tries GROMACS to warn me? Should I change something? That depends whether your molecule should have bonds this long in the configuration you provided to pdb2gmx... but since you've kept the nature of your molecule a mystery, you'll have to answer that yourself :-) In my .rtp parametrization file in the CHARMM27 folder I gave the equilibrium bond length in angstrom with corresponding force constant in kcal/mol, that are out of a supporting Information of a group, that made quantum mechanical calculations with my molecule. See chapter 2 for the acceptable gromacs units. These do not include Angstrom or kcal/mol. 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] grompp Unkown bond_atomtype C2
Hi After: pdb2gmx -f mymol.pdb -water tip3p editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro I typed: grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr where em.mdp is my energy minimization file and I got: Fatal error: Unknown bond_atomtype C2 What is here the problem? All atom types should be declared by me, I guess. Thanks for helping me Greetings Lara -- 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] Wierd results from Umbrella sampling
Dear Sir/Madam, I have performed umbrella pulling and umbrella sampling my protein from a DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve suddenly turns to zero at the last 1 nm) and the histograph does not show any overlap. Actually, I did it strictly based on Justin's tutorial, with the sample spacing of 0.2 nm. Here are some lines from the end of the energy file (The energy should not decrease since it was in summation): Distance(nm) Energy (Kcal/mol) 5.2883485.705318e+01 5.3162504.881724e+01 5.3441524.022505e+01 5.3720543.101854e+01 5.3999562.208200e+01 5.4278581.343340e+01 5.4557614.267619e+00 5.483663-5.084078e+00 ? minus 5.511565-1.486168e+01 ? minus 5.539467-2.393515e+01 ? minus 5.567369-3.343453e+01 ? minus Followings are some lines from the end of histograph file: Distance(nm) 5.4557610 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 5.4836630 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 5.5115650 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 5.5394670 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5.5673690 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 I am really depressed because it took me quiet a long time to sampling but it seems in vain... I really no idea to find out what went wrong. I am looking forward to your help. Thanks a lot. Jiangfeng. Jiangfeng Du, PhD Student Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 Mobile: +31-681741859 FAX: +31-43-3884159 6200 MD Maastricht The Netherlands-- 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] Test Particle Insertion
Thank you very much! I just saw your response.
As I run it in NPT ensemble the plot with volume is important for me.
Please, See the plot:
http://speedy.sh/CJn5b/tpiN.jpg
So does the fluctuating red curve make any sesnse then if it does not
consider volume?
Another thing: this is chemical potential of the system with extra water
molecule (N+1), right (u=-kTlog(Ve ^ (U*B)/(V))n+1? So if I want to obtain
the excess chemical potential:
u=-kTlog(Ve ^ (-deltaU*B)/(V)) I should calculate it for the system with N
molecules and then substract it.
Is it calculated somewhere or I should use g_energy of my previosu system
and calculate the total potential energy then -kTlog... of this values and
then substract it? Please correct me if I am wrong.
Steven
On Tue, May 15, 2012 at 11:59 AM, Javier Cerezo j...@um.es wrote:
Hi Steven.
1. Why this value is divided by nm3? Shall I multiply it by the
simulation box?
It is not not divided by nm3. The legend for y axis is not appropriate
for your plot. Keep in mind that the same graph is used to represent lots
of quantities (you can plot all of them with xmgrace -nxy tpi.xvg). The y
axis is not the same for all, but only one label is possible, so developers
have to chose which label to place on the axis. But this is just a label,
don't give much importance to it and analyse you results (including units)
according to the equations and the standard units in gromacs.
2. Why e^(-BU) is multiplied by V? I just want to have the excess
chemical potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get deltaU?
The volume appears in the expression of the excess chemical potential if
you are running a NpT ensemble. The second plot (if you use xmgrace -nxy
tpi.xvg) does not contain the volume.
3. The value corresponds to the plateau so I should run it for longer
time?
You are getting a timeensemble average and for large sampling (and large
simulation times), this average should converge. So, the final value you
will get is the last point of the graph, it up to you to say if it is
converged. So you can try to enlarge the number of points sampled, if the
shape does not change you are sampling correctly every snapshot, then take
longer simulation times if you want to converge your results.
Javier
El 15/05/12 09:57, Steven Neumann escribió:
On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 5/14/12 11:53 AM, Steven Neumann wrote:
Dear Gmx Users,
Did anyone use TPI method for the calculation of chemical potential? The
tpi.xvg
files consists of:
@ s0 legend -kT log(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4 legend f. Ue\S-\xb\f{}U\N
@ s5 legend f. U\sVdW System\Ne\S-\xb\f{}U\N
@ s6 legend f. U\sdisp c\Ne\S-\xb\f{}U\N
@ s7 legend f. U\sCoul System\Ne\S-\xb\f{}U\N
@ s8 legend f. U\sCoul recip\Ne\S-\xb\f{}U\N
@xaxis label Time (ps)
@yaxis label (kJ mol\S-1\N) / (nm\S3\N)
Can anyone explain me these legends? I just want obtain a value of the
excess
chemical potential according to the equation:
u=-kT log (-deltaV/kT), Which legend is responsible for this and what
are the
units? kJ/mol? Please, explain as the above letters does not mean to me
anything?
These strings are formatted for XmGrace. Have you tried plotting the
file to see what it contains? The legends will be far more obvious if you
do.
-Justin
Thank you Justin.
Can anyone explain me from the plot:
http://speedy.sh/Xpnws/tpi.JPG
1. Why this value is divided by nm3? Shall I multiply it by the simulation
box?
2. Why e^(-BU) is multiplied by V? I just want to have the excess chemical
potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get deltaU?
3. The value corresponds to the plateau so I should run it for longer time?
Thank you,
Steven
--
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
--
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Please search the archive at
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--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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Re: [gmx-users] Test Particle Insertion
About the red curve, I guess fluctuations might be directly related to
volume fluctuations, you can extract the volume over time from g_energy
(boxXX*boxYY**boxZZ) and compare. (just another comment, now I am not
very sure about the f. that precedes the red line legend..)
About the interpretation of the quantities, the Widom technique does not
provide you with an absolute value of the chemical potential but
directly with the excess chemical potential. So, mu=-kTlog(Ve ^
(U*B)/(V))n+1 is the excess chemical potential, where (if I recall
correctly) U_{n+1} is the the interaction energy between the inserted
particle and the rest of the system. You don't need (and should not do)
such post-processing operations that you proposed to get the excess
chemical potential.
Javier
El 16/05/12 11:06, Steven Neumann escribió:
Thank you very much! I just saw your response.
As I run it in NPT ensemble the plot with volume is important for me.
Please, See the plot:
http://speedy.sh/CJn5b/tpiN.jpg
So does the fluctuating red curve make any sesnse then if it does not
consider volume?
Another thing: this is chemical potential of the system with extra
water molecule (N+1), right (u=-kTlog(Ve ^ (U*B)/(V))n+1? So if I want
to obtain the excess chemical potential:
u=-kTlog(Ve ^ (-deltaU*B)/(V)) I should calculate it for the system
with N molecules and then substract it.
Is it calculated somewhere or I should use g_energy of my previosu
system and calculate the total potential energy then -kTlog... of this
values and then substract it? Please correct me if I am wrong.
Steven
On Tue, May 15, 2012 at 11:59 AM, Javier Cerezo j...@um.es
mailto:j...@um.es wrote:
Hi Steven.
1. Why this value is divided by nm3? Shall I multiply it by the
simulation box?
It is not not divided by nm3. The legend for y axis is not
appropriate for your plot. Keep in mind that the same graph is
used to represent lots of quantities (you can plot all of them
with xmgrace -nxy tpi.xvg). The y axis is not the same for all,
but only one label is possible, so developers have to chose which
label to place on the axis. But this is just a label, don't give
much importance to it and analyse you results (including units)
according to the equations and the standard units in gromacs.
2. Why e^(-BU) is multiplied by V? I just want to have the excess
chemical potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get
deltaU?
The volume appears in the expression of the excess chemical
potential if you are running a NpT ensemble. The second plot (if
you use xmgrace -nxy tpi.xvg) does not contain the volume.
3. The value corresponds to the plateau so I should run it for
longer time?
You are getting a timeensemble average and for large sampling
(and large simulation times), this average should converge. So,
the final value you will get is the last point of the graph, it up
to you to say if it is converged. So you can try to enlarge the
number of points sampled, if the shape does not change you are
sampling correctly every snapshot, then take longer simulation
times if you want to converge your results.
Javier
El 15/05/12 09:57, Steven Neumann escribió:
On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu wrote:
On 5/14/12 11:53 AM, Steven Neumann wrote:
Dear Gmx Users,
Did anyone use TPI method for the calculation of chemical
potential? The tpi.xvg
files consists of:
@ s0 legend -kT log(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4 legend f. Ue\S-\xb\f{}U\N
@ s5 legend f. U\sVdW System\Ne\S-\xb\f{}U\N
@ s6 legend f. U\sdisp c\Ne\S-\xb\f{}U\N
@ s7 legend f. U\sCoul System\Ne\S-\xb\f{}U\N
@ s8 legend f. U\sCoul recip\Ne\S-\xb\f{}U\N
@xaxis label Time (ps)
@yaxis label (kJ mol\S-1\N) / (nm\S3\N)
Can anyone explain me these legends? I just want obtain a
value of the excess
chemical potential according to the equation:
u=-kT log (-deltaV/kT), Which legend is responsible for
this and what are the
units? kJ/mol? Please, explain as the above letters does
not mean to me anything?
These strings are formatted for XmGrace. Have you tried
plotting the file to see what it contains? The legends will
be far more obvious if you do.
-Justin
Thank you Justin.
Can anyone explain me from the plot:
http://speedy.sh/Xpnws/tpi.JPG
1. Why this value is divided by nm3? Shall I multiply it by the
simulation box?
2. Why e^(-BU) is multiplied by V? I just want to have the excess
chemical
Re: [gmx-users] Questions about Thermostats
On Tue, 2012-05-15 at 19:47 +0100, Lara Bunte wrote: Hello To make better energy minimization procedures I read about thermostats and barostats. I understand the physical concepts and differences between global and local thermostats and the difference between Berendsen and Nose-Hoover thermostat. 1.) Maybe this question is a little bit hairsplitting, but: This concepts of thermostats and barostats, is this Thermodynamics, is this Kinetics, is this statistical physics? What is it if I want to give this a name. 2.) I read, that local thermostats, i.e. stochastic dynamics produce a NVT ensemble, which is a canonical ensemble and that this alway fulfills Ergodicity Theorem. About this I have following question: In my literature they said, that this means, that all degrees of freedom in the system are coupled strong enough each other. This confuses me. I learned, that ergodicity means, that the complete phase space is passed by a trajectory, if we wait long enough. This means, that ensemble average is equal to time average of the system. Where is in my statement about ergodicity the meaning of all degrees of freedom in the system are coupled strong enough Do this in fact mean, that the complete phase space is passed? 3.) I ask myself what I should use. First question: Local or global thermostat? I guess (not knowing, guessing), that global is better for energy minimization, because as far as I understand, it is more stable than local description. From a physical point of view I think Nose-Hoover shoul be always better, because it produces a real canonical ensemble, while Berendsen is microcanonical ensemble, which is totaly unrealistic?! In an microcanonical ensemble, energy is not changed with the enviroment. This makes no sense? Thanks for helping me Greetings Lara Hi, there has been recently a discussion about this topic on this mailing list. Check the archives for the information you look for. However, Berendsen is not producing any kind of known ensemble, and therefore only applicable for equilibration. /Flo -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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] Test Particle Insertion
On Wed, May 16, 2012 at 10:28 AM, Javier Cerezo j...@um.es wrote:
About the red curve, I guess fluctuations might be directly related to
volume fluctuations, you can extract the volume over time from g_energy
(boxXX*boxYY**boxZZ) and compare. (just another comment, now I am not very
sure about the f. that precedes the red line legend..)
About the interpretation of the quantities, the Widom technique does not
provide you with an absolute value of the chemical potential but directly
with the excess chemical potential. So, mu=-kTlog(Ve ^ (U*B)/(V))n+1 is the
excess chemical potential, where (if I recall correctly) U_{n+1} is the the
interaction energy between the inserted particle and the rest of the
system. You don't need (and should not do) such post-processing operations
that you proposed to get the excess chemical potential.
Javier
Thank you.
In this case I am considering the curve with NPT - with volume.
From the equation u=-kTlog(Ve ^ (U*B)/(V))n+1 (the one on the plot - if it
is correct! Or it should be with delta?) we will obtain the chemical
potential of the system with N+1 molecules. To obtain the excess we need to
have chemical potential of the system wit N particles and the substract it
according to the equation:
http://www.sklogwiki.org/SklogWiki/index.php/Widom_test-particle_method
If it is a mistake and there is deltaU this is the exceess, if not this is
only for N+1. Please, correct me if I am wrong.
Steven
El 16/05/12 11:06, Steven Neumann escribió:
Thank you very much! I just saw your response.
As I run it in NPT ensemble the plot with volume is important for me.
Please, See the plot:
http://speedy.sh/CJn5b/tpiN.jpg
So does the fluctuating red curve make any sesnse then if it does not
consider volume?
Another thing: this is chemical potential of the system with extra water
molecule (N+1), right (u=-kTlog(Ve ^ (U*B)/(V))n+1? So if I want to obtain
the excess chemical potential:
u=-kTlog(Ve ^ (-deltaU*B)/(V)) I should calculate it for the system with N
molecules and then substract it.
Is it calculated somewhere or I should use g_energy of my previosu system
and calculate the total potential energy then -kTlog... of this values and
then substract it? Please correct me if I am wrong.
Steven
On Tue, May 15, 2012 at 11:59 AM, Javier Cerezo j...@um.es wrote:
Hi Steven.
1. Why this value is divided by nm3? Shall I multiply it by the
simulation box?
It is not not divided by nm3. The legend for y axis is not appropriate
for your plot. Keep in mind that the same graph is used to represent lots
of quantities (you can plot all of them with xmgrace -nxy tpi.xvg). The y
axis is not the same for all, but only one label is possible, so developers
have to chose which label to place on the axis. But this is just a label,
don't give much importance to it and analyse you results (including units)
according to the equations and the standard units in gromacs.
2. Why e^(-BU) is multiplied by V? I just want to have the excess
chemical potential: u=-kTlog(e ^ (-deltaU*B) - so how can I get deltaU?
The volume appears in the expression of the excess chemical potential if
you are running a NpT ensemble. The second plot (if you use xmgrace -nxy
tpi.xvg) does not contain the volume.
3. The value corresponds to the plateau so I should run it for longer
time?
You are getting a timeensemble average and for large sampling (and
large simulation times), this average should converge. So, the final value
you will get is the last point of the graph, it up to you to say if it is
converged. So you can try to enlarge the number of points sampled, if the
shape does not change you are sampling correctly every snapshot, then take
longer simulation times if you want to converge your results.
Javier
El 15/05/12 09:57, Steven Neumann escribió:
On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul jalem...@vt.eduwrote:
On 5/14/12 11:53 AM, Steven Neumann wrote:
Dear Gmx Users,
Did anyone use TPI method for the calculation of chemical potential?
The tpi.xvg
files consists of:
@ s0 legend -kT log(Ve\S-\xb\f{}U\N/V)
@ s1 legend f. -kT loge\S-\xb\f{}U\N
@ s2 legend f. e\S-\xb\f{}U\N
@ s3 legend f. V
@ s4 legend f. Ue\S-\xb\f{}U\N
@ s5 legend f. U\sVdW System\Ne\S-\xb\f{}U\N
@ s6 legend f. U\sdisp c\Ne\S-\xb\f{}U\N
@ s7 legend f. U\sCoul System\Ne\S-\xb\f{}U\N
@ s8 legend f. U\sCoul recip\Ne\S-\xb\f{}U\N
@xaxis label Time (ps)
@yaxis label (kJ mol\S-1\N) / (nm\S3\N)
Can anyone explain me these legends? I just want obtain a value of the
excess
chemical potential according to the equation:
u=-kT log (-deltaV/kT), Which legend is responsible for this and what
are the
units? kJ/mol? Please, explain as the above letters does not mean to me
anything?
These strings are formatted for XmGrace. Have you tried plotting the
file to see what it contains? The legends will be far more obvious if you
do.
-Justin
[gmx-users] Spherical shaped box
Dear users, I am doing Protein Ligand simulation, increasing temp. from 100, 200, to 300 K. after 1ns of simulation in 300 K, the protein jumps out of the box and when I use the command trjconv_mpi -f *.trr -s *.tpr -o *new.trr -pbc nojump followed by trjconv_mpi -f new*.trr -s *.tpr -o new*.pdb -dump 1000 the box shape changes from dodecahedron to spherical. In Gromacs manual I read ; There are several possible shapes for space-filling unit cells. Some, as the rhombic dodecahedron and the truncated octahedron approach a spherical shape better than a cubic box and are therefore more economical for studying an (approximately spherical) macromolecule in solution, since less solvent molecules are required to fill the box given a minimum distance between macromolecular images... . Does it mean that it is ok and I can continue the simulation or I have to increase the box size? After simulation in 200 K the protein juped out of the box but using the same command the problem was fixed, without changing the box shape. Thank you in advance for the help Sogol-- 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] Minimization with DPOSRE
Dear Gmx Users, I would like to run energy minimization with some atoms restrained - this is a surface made of atoms which do not share any bonds. So the EM of water only. I tries to use define = -DPOSRES in my EM file but then the surface atoms change their positions. Thus, when I want to run NVT equilibration I got errors of water molecules which cannot be settled so EM is needed. Would you advise something? Steven -- 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] do_dssp segmentation fault error
Hello Friends I have installed GROMACS 4.5.5 on linux. I put the DSSP Executable in /usr/local/bin when i run the following command: do_dssp -s md.tpr -f md.trr -b 40 -e 50 -o fws_ss.xpm i got the following error. Reading file md.tpr, VERSION 4.5.5 (single precision) Reading file md.tpr, VERSION 4.5.5 (single precision) Segmentation fault Please tell me how can i resolve this Segmentation fault error. -- 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] Questions about Thermostats
Hi Florian, Hi, there has been recently a discussion about this topic on this mailing list. Check the archives for the information you look for. However, Berendsen is not producing any kind of known ensemble, and therefore only applicable for equilibration. That's a very strong statement, and scientifically unsound. From a theoretical statistical-mechanical perspective, the ensemble with the Berendsen thermostat does not fall into the known classes. This implies that using the Berendsen thermostat yields a physically different ensemble. Yet the relevant question is whether the ensemble is statistically significantly different, or even practically significantly different. A next question is whether the difference between two simulations with the Berendsen thermostat and two simulations with one of the other ones is consistent or not. And when comparing with experiments, are the predictions with the Berendsen thermostat different from one of the others? This would be a very nice matter of debate if there was a difference in performance using different thermostats. However (unfortunately? ;)) there is not. So for the same cost there are thermostats that do produce the desired ensemble, which makes these preferable over the one from Berendsen (also for equilibration). That is not the same as stating that it is only applicable for equilibration though. For the barostat it's a bit more complicated. Parrinello-Rahman can not be used for equilibration, because a large deviation from the target pressure may well cause large fluctuations that are unphysical and may cause instability. So at the moment the Berendsen barostat appears the only _one_ applicable for equilibration, but that doesn't (yet) disqualify it for further use. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Spherical shaped box
Hi Sogol, You remove jumps over periodic boundary conditions, giving a continuous trajectory. That gives you a very nice view on diffusion in your system, which happens to be equal in all directions. Hence, the end result looks spherical. But that's not the same as having a spherical box. If you draw the box in VMD or Pymol, you'll see it's still close to the original (triclinic) shape, but has become a bit small in relation to your molecules. Cheers, Tsjerk On Wed, May 16, 2012 at 11:49 AM, Kowsar Bagherzadeh kw_bagherza...@yahoo.com wrote: Dear users, I am doing Protein Ligand simulation, increasing temp. from 100, 200, to 300 K. after 1ns of simulation in 300 K, the protein jumps out of the box and when I use the command trjconv_mpi -f *.trr -s *.tpr -o *new.trr -pbc nojump followed by trjconv_mpi -f new*.trr -s *.tpr -o new*.pdb -dump 1000 the box shape changes from dodecahedron to spherical. In Gromacs manual I read ; There are several possible shapes for space-filling unit cells. Some, as the rhombic dodecahedron and the truncated octahedron approach a spherical shape better than a cubic box and are therefore more economical for studying an (approximately spherical) macromolecule in solution, since less solvent molecules are required to fill the box given a minimum distance between macromolecular images... . Does it mean that it is ok and I can continue the simulation or I have to increase the box size? After simulation in 200 K the protein juped out of the box but using the same command the problem was fixed, without changing the box shape. Thank you in advance for the help Sogol -- gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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] Test Particle Insertion
Hi
Well, according to the link you pointed out, the Widom technique gives
you the excess chemical potential, as we discussed. mu and mu_ideal (in
your link) are not calculated, those are just the reference states
between which the Widom technique calculates the excess chem pot.
As I said, I think U_{n+1} refers to the interaction energy of the
inserte particle with the system, but maybe someone could confirm or
correct.
Javier
El 16/05/12 11:44, Steven Neumann escribió:
On Wed, May 16, 2012 at 10:28 AM, Javier Cerezo j...@um.es
mailto:j...@um.es wrote:
About the red curve, I guess fluctuations might be directly
related to volume fluctuations, you can extract the volume over
time from g_energy (boxXX*boxYY**boxZZ) and compare. (just another
comment, now I am not very sure about the f. that precedes the
red line legend..)
About the interpretation of the quantities, the Widom technique
does not provide you with an absolute value of the chemical
potential but directly with the excess chemical potential. So,
mu=-kTlog(Ve ^ (U*B)/(V))n+1 is the excess chemical potential,
where (if I recall correctly) U_{n+1} is the the interaction
energy between the inserted particle and the rest of the system.
You don't need (and should not do) such post-processing operations
that you proposed to get the excess chemical potential.
Javier
Thank you.
In this case I am considering the curve with NPT - with volume.
From the equation u=-kTlog(Ve ^ (U*B)/(V))n+1 (the one on the plot -
if it is correct! Or it should be with delta?) we will obtain the
chemical potential of the system with N+1 molecules. To obtain the
excess we need to have chemical potential of the system wit N
particles and the substract it according to the
equation:http://www.sklogwiki.org/SklogWiki/index.php/Widom_test-particle_method
If it is a mistake and there is deltaU this is the exceess, if not
this is only for N+1. Please, correct me if I am wrong.
Steven
El 16/05/12 11:06, Steven Neumann escribió:
Thank you very much! I just saw your response.
As I run it in NPT ensemble the plot with volume is important for
me. Please, See the plot:
http://speedy.sh/CJn5b/tpiN.jpg
So does the fluctuating red curve make any sesnse then if it does
not consider volume?
Another thing: this is chemical potential of the system with
extra water molecule (N+1), right (u=-kTlog(Ve ^ (U*B)/(V))n+1?
So if I want to obtain the excess chemical potential:
u=-kTlog(Ve ^ (-deltaU*B)/(V)) I should calculate it for the
system with N molecules and then substract it.
Is it calculated somewhere or I should use g_energy of my
previosu system and calculate the total potential energy then
-kTlog... of this values and then substract it? Please correct me
if I am wrong.
Steven
On Tue, May 15, 2012 at 11:59 AM, Javier Cerezo j...@um.es
mailto:j...@um.es wrote:
Hi Steven.
1. Why this value is divided by nm3? Shall I multiply it by
the simulation box?
It is not not divided by nm3. The legend for y axis is not
appropriate for your plot. Keep in mind that the same graph
is used to represent lots of quantities (you can plot all of
them with xmgrace -nxy tpi.xvg). The y axis is not the same
for all, but only one label is possible, so developers have
to chose which label to place on the axis. But this is just a
label, don't give much importance to it and analyse you
results (including units) according to the equations and the
standard units in gromacs.
2. Why e^(-BU) is multiplied by V? I just want to have the
excess chemical potential: u=-kTlog(e ^ (-deltaU*B) - so how
can I get deltaU?
The volume appears in the expression of the excess chemical
potential if you are running a NpT ensemble. The second plot
(if you use xmgrace -nxy tpi.xvg) does not contain the volume.
3. The value corresponds to the plateau so I should run it
for longer time?
You are getting a timeensemble average and for large
sampling (and large simulation times), this average should
converge. So, the final value you will get is the last point
of the graph, it up to you to say if it is converged. So you
can try to enlarge the number of points sampled, if the shape
does not change you are sampling correctly every snapshot,
then take longer simulation times if you want to converge
your results.
Javier
El 15/05/12 09:57, Steven Neumann escribió:
On Mon, May 14, 2012 at 5:05 PM, Justin A. Lemkul
jalem...@vt.edu mailto:jalem...@vt.edu wrote:
On 5/14/12 11:53 AM, Steven Neumann wrote:
Dear Gmx Users,
Did anyone use TPI method for the calculation of
Re: [gmx-users] TFE Proper Dihedral types...
On 5/16/12 12:36 AM, rama david wrote: On Tue, May 15, 2012 at 10:24 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: The parameters are missing from ffbonded.itp, making the implementation incomplete. You can obtain a TFE topology from ATB: http://compbio.biosci.uq.edu.__au/atb/download.py?molid=1655 http://compbio.biosci.uq.edu.au/atb/download.py?molid=1655 -Justin Thank you Justin .. I obtain the topology from given link.. 1. If you have some time , Could you tell me the way how to fix the missing parameter from ffbonded.itp ..??? Look in the topology from ATB to see how it should be treated. -Justin -- Justin A. Lemkul, Ph.D. 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] Coupling groups in protein-ligand-lipid simulation
On 5/16/12 1:01 AM, Anirban wrote: Hi ALL, I am simulating a membrane protein docked with a ligand and embedded in a lipid bilayer. For COM removal I am using two groups, Prt_Lig_Lipid and SOL_CL. For temperature and pressure couplings should I use these two groups or should I use three groups, Protein, Lipid and Lig_SOL_CL? Any suggestion is welcome. If the ligand is bound to the protein, I would couple the protein and ligand as a single group. -Justin -- Justin A. Lemkul, Ph.D. 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] Questions about Thermostats
Hi Tsjerk, sorry for the strong statement. I should have said: should be applied ... instead of only applicable. You are right, the question is how big is the difference and actually one would also expect, that the differences vanish with 1/N. However, so far it is unknown, what kind of distributions Berendsen does produce and how this is related to the true canonical ensemble. For this reason, I would be very catious. In my studies I realized big differences in density and dynamical properties, if Berendsen instead of PR is used. Cheers, Flo On Wed, 2012-05-16 at 12:11 +0200, Tsjerk Wassenaar wrote: Hi Florian, Hi, there has been recently a discussion about this topic on this mailing list. Check the archives for the information you look for. However, Berendsen is not producing any kind of known ensemble, and therefore only applicable for equilibration. That's a very strong statement, and scientifically unsound. From a theoretical statistical-mechanical perspective, the ensemble with the Berendsen thermostat does not fall into the known classes. This implies that using the Berendsen thermostat yields a physically different ensemble. Yet the relevant question is whether the ensemble is statistically significantly different, or even practically significantly different. A next question is whether the difference between two simulations with the Berendsen thermostat and two simulations with one of the other ones is consistent or not. And when comparing with experiments, are the predictions with the Berendsen thermostat different from one of the others? This would be a very nice matter of debate if there was a difference in performance using different thermostats. However (unfortunately? ;)) there is not. So for the same cost there are thermostats that do produce the desired ensemble, which makes these preferable over the one from Berendsen (also for equilibration). That is not the same as stating that it is only applicable for equilibration though. For the barostat it's a bit more complicated. Parrinello-Rahman can not be used for equilibration, because a large deviation from the target pressure may well cause large fluctuations that are unphysical and may cause instability. So at the moment the Berendsen barostat appears the only _one_ applicable for equilibration, but that doesn't (yet) disqualify it for further use. Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Florian Dommert Dipl. - Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: domm...@icp.uni-stuttgart.de Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert Tel.: +49 - (0)711 - 68563613 Fax.: +49 - (0)711 - 68563658 signature.asc Description: This is a digitally signed message part -- 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] charge and ionization state at pH 6.5
Dear All, Will you please tell me how GROMACS calculates the total charge of a protein at pH 6.5? And how do we assign the ionization state of the residues, especially for HIS at pH 6.5? I am looking forward to getting a reply from you. Cheers, Acoot-- 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] do_dssp segmentation fault error
On 5/16/12 5:57 AM, bunty xy wrote: Hello Friends I have installed GROMACS 4.5.5 on linux. I put the DSSP Executable in /usr/local/bin when i run the following command: do_dssp -s md.tpr -f md.trr -b 40 -e 50 -o fws_ss.xpm i got the following error. Reading file md.tpr, VERSION 4.5.5 (single precision) Reading file md.tpr, VERSION 4.5.5 (single precision) Segmentation fault Please tell me how can i resolve this Segmentation fault error. This same question was posed just a little bit earlier. You need to make sure you're using the right version of DSSP (the old one). -Justin -- Justin A. Lemkul, Ph.D. 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] Minimization with DPOSRE
On 5/16/12 5:54 AM, Steven Neumann wrote: Dear Gmx Users, I would like to run energy minimization with some atoms restrained - this is a surface made of atoms which do not share any bonds. So the EM of water only. I tries to use define = -DPOSRES in my EM file but then the surface atoms change their positions. Thus, when I want to run NVT equilibration I got errors of water molecules which cannot be settled so EM is needed. Would you advise something? Restraints do not guarantee that atoms won't move. They are simply a biasing force that disfavors motion. Either apply a stronger force constant for the restraints or use freezegrps to fix the atomic positions. -Justin -- Justin A. Lemkul, Ph.D. 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] charge and ionization state at pH 6.5
On 5/16/12 7:13 AM, Acoot Brett wrote: Dear All, Will you please tell me how GROMACS calculates the total charge of a protein at pH 6.5? And how do we assign the ionization state of the residues, especially for HIS at pH 6.5? Gromacs does not automatically deal with anything aside from pH 7 protonation states, though for most residues the difference between 6.5 and 7 is irrelevant. Histidine protonation is assigned based on a hydrogen bonding search. If you need to adjust protonation states, you need to do so yourself, but at pH 6.5 it will be very tricky to deal with those histidines. -Justin -- Justin A. Lemkul, Ph.D. 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] grompp Unkown bond_atomtype C2
On 5/16/12 3:56 AM, Lara Bunte wrote: Hi After: pdb2gmx -f mymol.pdb -water tip3p editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro I typed: grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr where em.mdp is my energy minimization file and I got: Fatal error: Unknown bond_atomtype C2 What is here the problem? All atom types should be declared by me, I guess. You're making use of an atom type called C2 in some bonded interaction, but such an atom type doesn't exist. You need to define it. -Justin -- Justin A. Lemkul, Ph.D. 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] grompp Unkown bond_atomtype C2
Hi in my .rtp file I wrote in the [ atoms ] block C2 CN1A 0.7481 1 but in the atomtypes.atp file I wrote CN1A 12.01100 So I declared it. So what do you mean with such an atom type doesn't exist? Greetings Lara - Ursprüngliche Message - Von: Justin A. Lemkul jalem...@vt.edu An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users gmx-users@gromacs.org CC: Gesendet: 13:22 Mittwoch, 16.Mai 2012 Betreff: Re: [gmx-users] grompp Unkown bond_atomtype C2 On 5/16/12 3:56 AM, Lara Bunte wrote: Hi After: pdb2gmx -f mymol.pdb -water tip3p editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro I typed: grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr where em.mdp is my energy minimization file and I got: Fatal error: Unknown bond_atomtype C2 What is here the problem? All atom types should be declared by me, I guess. You're making use of an atom type called C2 in some bonded interaction, but such an atom type doesn't exist. You need to define it. -Justin -- Justin A. Lemkul, Ph.D. 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] grompp Unkown bond_atomtype C2
On 5/16/12 8:05 AM, Lara Bunte wrote: Hi in my .rtp file I wrote in the [ atoms ] block C2 CN1A0.7481 1 but in the atomtypes.atp file I wrote CN1A12.01100 So I declared it. So what do you mean with such an atom type doesn't exist? Neither of those actions constitutes what you need. Your atom name is C2, while its type is CN1A. Apparently somewhere in the bonded parameters you've assigned C2 as a type, which is wrong. You need to be using CN1A if adding a new bonded parameter. The CN1A atom type already exists in the force field so you don't need to do anything special. Note for the future that in order to add a new atom type (if necessary), it needs to have its parameters listed in ffbonded.itp. Mentioning it in the .rtp and .atp files does not do much for you; it simply makes that atom type accessible in the topology, but if it doesn't have parameters assigned, it is useless. -Justin -- Justin A. Lemkul, Ph.D. 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] Wierd results from Umbrella sampling
On 5/16/12 4:08 AM, Du Jiangfeng (BIOCH) wrote: Dear Sir/Madam, I have performed umbrella pulling and umbrella sampling my protein from a DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve suddenly turns to zero at the last 1 nm) and the histograph does not show any overlap. Actually, I did it strictly based on Justin's tutorial, with the sample spacing of 0.2 nm. Please note that the exact protocol in the tutorial may or may not be applicable to all systems. The overall workflow is the same, but details regarding use of groups, .mdp files, etc may vary. Here are some lines from the end of the energy file (The energy should not decrease since it was in summation): Distance(nm) Energy (Kcal/mol) 5.2883485.705318e+01 5.316250 4.881724e+01 5.3441524.022505e+01 5.372054 3.101854e+01 5.399956 2.208200e+01 5.427858 1.343340e+01 5.455761 4.267619e+00 5.483663 -5.084078e+00 ? minus 5.511565 -1.486168e+01 ? minus 5.539467 -2.393515e+01 ? minus 5.567369 -3.343453e+01 ? minus What energetic term is this? A summation can decrease if the values being added are all negative. Followings are some lines from the end of histograph file: Distance(nm) 5.455761 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 5.483663 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 5.511565 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 5.539467 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5.567369 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 I am really depressed because it took me quiet a long time to sampling but it seems in vain... I really no idea to find out what went wrong. Nor do we. What is in your .mdp file? How many windows are you using? What is the total desired length of the reaction coordinate, and what are the initial and final COM distances that you are restraining? What are your box dimensions? -Justin -- Justin A. Lemkul, Ph.D. 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
[gmx-users] (no subject)
Hi Gromacs Friends, I plan to simulate protein In Trifluoro Ethanol solvent using G96 53a6 FF Please help to define parameters in md.mdp For water I am using following mdp file lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 0.9; short-range neighborlist cutoff (in nm) rcoulomb= 0.9; short-range electrostatic cutoff (in nm) vdw-type= Cut-off rvdw= 1.4; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME For TFE and water mix of different conc , What should be the mdp file parameter ??? I am using following ones.. Twin range cutt-off for nnonbonded interactions.. Short range cut-off 0.8 and long range 1.4 for both coulombic and lennard-jones Short range updates for every 5 step togather with pair list.. Please give me valuable suggestion .. Thank you in advance .. With Best Wishes, Rama David -- 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] (no subject)
On 5/16/12 8:49 AM, rama david wrote: Hi Gromacs Friends, I plan to simulate protein In Trifluoro Ethanol solvent using G96 53a6 FF Please help to define parameters in md.mdp For water I am using following mdp file lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 0.9; short-range neighborlist cutoff (in nm) rcoulomb= 0.9; short-range electrostatic cutoff (in nm) vdw-type= Cut-off rvdw= 1.4; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME For TFE and water mix of different conc , What should be the mdp file parameter ??? I am using following ones.. Twin range cutt-off for nnonbonded interactions.. Short range cut-off 0.8 and long range 1.4 for both coulombic and lennard-jones Short range updates for every 5 step togather with pair list.. Please give me valuable suggestion .. The settings given in an .mdp file are dependent upon the force field, not the molecules in the system. So if you have water or water/TFE, the requirements of the force field are still the same. -Justin -- Justin A. Lemkul, Ph.D. 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
[gmx-users] forcefields for lipids
Dear gmx users, Which force fields are suggested for lipids? Except CHARMM, any other forcefields? Anybody may suggest me articles in this about? Thanks in advance Sincerely, Shima-- 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] forcefields for lipids
Off the top of my head: There are the Berger lipids for the gromos FFs (Justin's tutorial) There was a B2 Adrenergic receptor paper that used Amber. and of course Martini appears to be everyone's favorite coarse grain FF. The literature search shall be left as an exercise for the reader. (You can even use google to search this mailing list or mirrors of it) On 2012-05-16 05:59:22AM -0700, Shima Arasteh wrote: Dear gmx users, Which force fields are suggested for lipids? Except CHARMM, any other forcefields? Anybody may suggest me articles in this about? Thanks in advance Sincerely, Shima -- 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 -- == Peter C. Lai| University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu| Birmingham AL 35294-4461 (205) 690-0808 | == -- 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] Wierd results from Umbrella sampling
One thought from justins post in the past, Look at the .trj in VMD with the unit cell box and see if something sticks out at the end (ie comes up in the bootmn of the box from the top). It then does what you show, however it may not be that. If it is, you'll have to increase your box deminsion in the pull dir. and re-run it or throw out the data after it turns negative... Steve Original-Nachricht Datum: Wed, 16 May 2012 10:08:06 +0200 Von: Du Jiangfeng (BIOCH) j...@maastrichtuniversity.nl An: gmx-users@gromacs.org gmx-users@gromacs.org Betreff: [gmx-users] Wierd results from Umbrella sampling Dear Sir/Madam, I have performed umbrella pulling and umbrella sampling my protein from a DOPC/DOPS membrane. Unfortunately, the results are really bad (Energy curve suddenly turns to zero at the last 1 nm) and the histograph does not show any overlap. Actually, I did it strictly based on Justin's tutorial, with the sample spacing of 0.2 nm. Here are some lines from the end of the energy file (The energy should not decrease since it was in summation): Distance(nm) Energy (Kcal/mol) 5.288348 5.705318e+01 5.316250 4.881724e+01 5.344152 4.022505e+01 5.372054 3.101854e+01 5.399956 2.208200e+01 5.427858 1.343340e+01 5.455761 4.267619e+00 5.483663 -5.084078e+00 ? minus 5.511565 -1.486168e+01 ? minus 5.539467 -2.393515e+01 ? minus 5.567369 -3.343453e+01 ? minus Followings are some lines from the end of histograph file: Distance(nm) 5.455761 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 5.483663 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 5.511565 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 5.539467 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5.567369 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 I am really depressed because it took me quiet a long time to sampling but it seems in vain... I really no idea to find out what went wrong. I am looking forward to your help. Thanks a lot. Jiangfeng. Jiangfeng Du, PhD Student Cardiovascular Research Institute Maastricht Department of Biochemistry P.O. Box 616 Mobile: +31-681741859 FAX: +31-43-3884159 6200 MD Maastricht The Netherlands-- 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 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- 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] forcefields for lipids
On 5/16/12 9:06 AM, Peter C. Lai wrote: Off the top of my head: There are the Berger lipids for the gromos FFs (Justin's tutorial) There was a B2 Adrenergic receptor paper that used Amber. and of course Martini appears to be everyone's favorite coarse grain FF. There is also an OPLS-AA formulation of lipid parameters, and ways to combine OPLS-AA representations of proteins with the Berger lipids. -Justin The literature search shall be left as an exercise for the reader. (You can even use google to search this mailing list or mirrors of it) On 2012-05-16 05:59:22AM -0700, Shima Arasteh wrote: Dear gmx users, Which force fields are suggested for lipids? Except CHARMM, any other forcefields? Anybody may suggest me articles in this about? Thanks in advance Sincerely, Shima -- 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 -- Justin A. Lemkul, Ph.D. 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] forcefields for lipids
Hi, In addition to the ones already mentioned (CHARMM, GAFF/AMBER, Berger, OPLS-AA) there are several united-atom GROMOS based lipid forcefields (43A1-S3, 53A6L/54A7, 53A6 Kukol, etc.). The Lipidbook website is a useful place to find lots of lipid parameters in one location: http://lipidbook.bioch.ox.ac.uk/ The choice of force field will depend upon what you wish to simulate. With PC lipids there are more force fields available compared to other phospholipids, so your choice of lipid may dictate your choice of force field. Additionally some of the available lipid force fields may work well for one type of lipid but not another. Finally if you have a membrane-protein system you also need to consider the combination with an appropriate protein force field. Cheers Tom Peter C. Lai wrote: Off the top of my head: There are the Berger lipids for the gromos FFs (Justin's tutorial) There was a B2 Adrenergic receptor paper that used Amber. and of course Martini appears to be everyone's favorite coarse grain FF. The literature search shall be left as an exercise for the reader. (You can even use google to search this mailing list or mirrors of it) On 2012-05-16 05:59:22AM -0700, Shima Arasteh wrote: Dear gmx users, Which force fields are suggested for lipids? Except CHARMM, any other forcefields? Anybody may suggest me articles in this about? Thanks in advance Sincerely, Shima -- 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 -- Dr Thomas Piggot University of Southampton, UK. -- 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] forcefields for lipids
Thanks for all your suggestions. Honestly, I want to simulate a protein-membrane system. My chosen membrane is POPC. After the simulation of the system, I'm gonna apply the umbrella sampling on the system to study the ion conduction through the channel composed of this protein. Before this, I had seen that the ion conduction through the gramicidin A channel in a bilayer were studied using CHARMM. Refer to that article I guess the CHARMM may give me the best out put. Is this an acceptable choice of a force field? Sincerely, Shima From: Thomas Piggot t.pig...@soton.ac.uk To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, May 16, 2012 5:55 PM Subject: Re: [gmx-users] forcefields for lipids Hi, In addition to the ones already mentioned (CHARMM, GAFF/AMBER, Berger, OPLS-AA) there are several united-atom GROMOS based lipid forcefields (43A1-S3, 53A6L/54A7, 53A6 Kukol, etc.). The Lipidbook website is a useful place to find lots of lipid parameters in one location: http://lipidbook.bioch.ox.ac.uk/ The choice of force field will depend upon what you wish to simulate. With PC lipids there are more force fields available compared to other phospholipids, so your choice of lipid may dictate your choice of force field. Additionally some of the available lipid force fields may work well for one type of lipid but not another. Finally if you have a membrane-protein system you also need to consider the combination with an appropriate protein force field. Cheers Tom Peter C. Lai wrote: Off the top of my head: There are the Berger lipids for the gromos FFs (Justin's tutorial) There was a B2 Adrenergic receptor paper that used Amber. and of course Martini appears to be everyone's favorite coarse grain FF. The literature search shall be left as an exercise for the reader. (You can even use google to search this mailing list or mirrors of it) On 2012-05-16 05:59:22AM -0700, Shima Arasteh wrote: Dear gmx users, Which force fields are suggested for lipids? Except CHARMM, any other forcefields? Anybody may suggest me articles in this about? Thanks in advance Sincerely, Shima -- gmx-users mailing list gmx-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 -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing list gmx-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] bonded interactions as table
Hi all, I have learned from manual that non bonded interactions can be given as user defined potential by using tables. If i want to give dihedral term as user defined potential keeping rest of the bonded parameters in their usual form, how can i do that. Please suggest me a way, Thanks Regards, Mohan -- 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] PMF profile from Umbrella - Plateau
On 5/16/12 10:25 AM, Steven Neumann wrote: Dear Justin, I pulled my ligad away of 6nm from the protein and obtained beautiful and smooth curve of PMF using 28 windows. Starting from zero kcal/mol corresponding to app 0.3 nm then minima and curve increase till my plateau which starts from app 1 nm - then I have nearly straight line till 6.3 nm. My question: Can I decrease pulling distance to save time for the future simualtions with this system in terms of number of water molecules? Shall I just pull it away of 2-3 nm and I will obtain the same deltaG? Ideally, one would separate the molecules such that they are no longer interacting. Obviously with methods like PME this is impossible, so what you're after is sufficient separation such that there is negligible interaction between the protein and ligand. The required distance depends on the nature and size of the ligand, the types of interactions it experiences, and the cutoffs used. Keep in mind that even if a molecule is beyond the longest nonbonded cutoff, there are still effects like water ordering that can persist up to about 1.0 nm, so I would certainly make sure that all the atoms of the ligand and protein are separated by a minimum of twice the longest cutoff or so to account for this effect. Note that this would imply the use of g_mindist, not g_dist, as the distance I'm talking about is not the same as the COM distance. That's just my own rule of thumb for an initial check; you'll have to analyze your own system to decide what's happening and what you should do. -Justin -- Justin A. Lemkul, Ph.D. 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] bonded interactions as table
On 5/16/12 10:34 AM, mohan maruthi sena wrote: Hi all, I have learned from manual that non bonded interactions can be given as user defined potential by using tables. If i want to give dihedral term as user defined potential keeping rest of the bonded parameters in their usual form, how can i do that. See manual section 4.2.13. Supplying a suitable table_d*.xvg file, with appropriate references to the tabulated function type (discussed in the manual) should be what you need. -Justin -- Justin A. Lemkul, Ph.D. 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
[gmx-users] umbrella sampling on GPU
Hello, I am using Gromacs 4.5 to perform umbrella sampling on CPU. I know that right now the GPU implementation does not support any pull code. Is it going to be available soon? Are angular restraints going to be supported as well? Thank you -- Diana Fusco Graduate Student Computational Biology and Bioinformatics Duke University -- 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] PMF profile from Umbrella - Plateau
On 5/16/12 11:16 AM, Steven Neumann wrote: On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/16/12 10:25 AM, Steven Neumann wrote: Dear Justin, I pulled my ligad away of 6nm from the protein and obtained beautiful and smooth curve of PMF using 28 windows. Starting from zero kcal/mol corresponding to app 0.3 nm then minima and curve increase till my plateau which starts from app 1 nm - then I have nearly straight line till 6.3 nm. My question: Can I decrease pulling distance to save time for the future simualtions with this system in terms of number of water molecules? Shall I just pull it away of 2-3 nm and I will obtain the same deltaG? Ideally, one would separate the molecules such that they are no longer interacting. Obviously with methods like PME this is impossible, so what you're after is sufficient separation such that there is negligible interaction between the protein and ligand. The required distance depends on the nature and size of the ligand, the types of interactions it experiences, and the cutoffs used. Keep in mind that even if a molecule is beyond the longest nonbonded cutoff, there are still effects like water ordering that can persist up to about 1.0 nm, so I would certainly make sure that all the atoms of the ligand and protein are separated by a minimum of twice the longest cutoff or so to account for this effect. Note that this would imply the use of g_mindist, not g_dist, as the distance I'm talking about is not the same as the COM distance. That's just my own rule of thumb for an initial check; you'll have to analyze your own system to decide what's happening and what you should do. -Justin Thanks Justin! I totally agree. But now having my ligand pulled 6 nm away and obtained deltaG= -4.5 kcal/mol. In theory when I use all windows till 3.5 nm (not till 6.3 nm) and I will obtain the same value it means that I can decrease the pulling distance in future simulations. Am I right? In theory, as long as you've satisfied yourself that this constitutes a sufficient representation of a non-interacting state, or as close to it as one can achieve in a system of finite size. I've already said what I think are reasonable criteria for a preliminary assessment; it's up to you to convince anyone reading your work that such measurements are sound and appropriate. -Justin -- Justin A. Lemkul, Ph.D. 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] PMF profile from Umbrella - Plateau
On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/16/12 10:25 AM, Steven Neumann wrote: Dear Justin, I pulled my ligad away of 6nm from the protein and obtained beautiful and smooth curve of PMF using 28 windows. Starting from zero kcal/mol corresponding to app 0.3 nm then minima and curve increase till my plateau which starts from app 1 nm - then I have nearly straight line till 6.3 nm. My question: Can I decrease pulling distance to save time for the future simualtions with this system in terms of number of water molecules? Shall I just pull it away of 2-3 nm and I will obtain the same deltaG? Ideally, one would separate the molecules such that they are no longer interacting. Obviously with methods like PME this is impossible, so what you're after is sufficient separation such that there is negligible interaction between the protein and ligand. The required distance depends on the nature and size of the ligand, the types of interactions it experiences, and the cutoffs used. Keep in mind that even if a molecule is beyond the longest nonbonded cutoff, there are still effects like water ordering that can persist up to about 1.0 nm, so I would certainly make sure that all the atoms of the ligand and protein are separated by a minimum of twice the longest cutoff or so to account for this effect. Note that this would imply the use of g_mindist, not g_dist, as the distance I'm talking about is not the same as the COM distance. That's just my own rule of thumb for an initial check; you'll have to analyze your own system to decide what's happening and what you should do. -Justin Thanks Justin! I totally agree. But now having my ligand pulled 6 nm away and obtained deltaG= -4.5 kcal/mol. In theory when I use all windows till 3.5 nm (not till 6.3 nm) and I will obtain the same value it means that I can decrease the pulling distance in future simulations. Am I right? Steven -- ==**== Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] PMF profile from Umbrella - Plateau
On Wed, May 16, 2012 at 4:20 PM, Justin A. Lemkul jalem...@vt.edu wrote: On 5/16/12 11:16 AM, Steven Neumann wrote: On Wed, May 16, 2012 at 3:38 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: On 5/16/12 10:25 AM, Steven Neumann wrote: Dear Justin, I pulled my ligad away of 6nm from the protein and obtained beautiful and smooth curve of PMF using 28 windows. Starting from zero kcal/mol corresponding to app 0.3 nm then minima and curve increase till my plateau which starts from app 1 nm - then I have nearly straight line till 6.3 nm. My question: Can I decrease pulling distance to save time for the future simualtions with this system in terms of number of water molecules? Shall I just pull it away of 2-3 nm and I will obtain the same deltaG? Ideally, one would separate the molecules such that they are no longer interacting. Obviously with methods like PME this is impossible, so what you're after is sufficient separation such that there is negligible interaction between the protein and ligand. The required distance depends on the nature and size of the ligand, the types of interactions it experiences, and the cutoffs used. Keep in mind that even if a molecule is beyond the longest nonbonded cutoff, there are still effects like water ordering that can persist up to about 1.0 nm, so I would certainly make sure that all the atoms of the ligand and protein are separated by a minimum of twice the longest cutoff or so to account for this effect. Note that this would imply the use of g_mindist, not g_dist, as the distance I'm talking about is not the same as the COM distance. That's just my own rule of thumb for an initial check; you'll have to analyze your own system to decide what's happening and what you should do. -Justin Thanks Justin! I totally agree. But now having my ligand pulled 6 nm away and obtained deltaG= -4.5 kcal/mol. In theory when I use all windows till 3.5 nm (not till 6.3 nm) and I will obtain the same value it means that I can decrease the pulling distance in future simulations. Am I right? In theory, as long as you've satisfied yourself that this constitutes a sufficient representation of a non-interacting state, or as close to it as one can achieve in a system of finite size. I've already said what I think are reasonable criteria for a preliminary assessment; it's up to you to convince anyone reading your work that such measurements are sound and appropriate. -Justin Thanks. Well, as my cutoff is 1.4 nm pulling 3.5 nm will suffice - and having the same value in the example makes reasonable argument for pulling e.g. 4nm to be on the safe side. Steven -- ==**== Justin A. Lemkul, Ph.D. Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://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] Index selection in g_potential
Hi, I am using the utility g_potential. It takes (among other files) an index file. At the beginning of the run, it prompts me for a selection from the index file. Is it possible to make more than one selection, such that the potential is calculated for each selection, _separately_? If I enter something like this: 0 3 11 The output seems to only include the potential due to the first selection (0) and seems to ignore the others. Thanks for your time! Andrew DeYoung Carnegie Mellon University -- 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] Index selection in g_potential
On 5/16/12 11:30 AM, Andrew DeYoung wrote: Hi, I am using the utility g_potential. It takes (among other files) an index file. At the beginning of the run, it prompts me for a selection from the index file. Is it possible to make more than one selection, such that the potential is calculated for each selection, _separately_? If I enter something like this: 0 3 11 The output seems to only include the potential due to the first selection (0) and seems to ignore the others. If you want multiple groups analyzed, you have to invoke g_potential multiple times, providing the different groups (individually) each time. -Justin -- Justin A. Lemkul, Ph.D. 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
[gmx-users] CM3 pont charges
Hi Guys You know any porgram that can be used to derrive CM3 point charges thanks Milinda Samaraweera University of Connecticut Department of Chemistry 55 N Eagleville road unit 3060 Storrs CT USA-- 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] Tabulated potentials for the Dihedrals - regd
Dear Gromacs users, I am using tabulated potentials for dihedrals of my system which is of form dih = (1/2)*K[COS n(phi-phi0)], Here n=3. I have generated table_d0.xvg by uniformly varying phi as 0.1 from -180 to 180 and calculated the numerical derivative and force by using the relations der = Y(n+1)- Y(n-1)/ (2*h) ; force = -der ; Here h = step size (i.e 0.1 in my case). Here I have some doubts: 1) Am I using the correct relations for calculation of derivative and force. 2) which value should we take for the k ( force constant) in ffbonded.itp, the value of k that specified with the dihedral potential ? or some arbitrary number ? As I have used the value of k given with the dihedral function in calculations of potential and the force, Is it necessary to mention force constant value again in ffbonded.itp and 3) if I run mdrun as mdrun -tableb table_do.xvg it giving the error : Library file table_d0_d0.xvg not found in current dir nor in default directories. Can you please suggest me the correct way of using the -tableb option in the case of multiple tables. Thank you in advance, Regards, Ramesh Cheerla. -- 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] itp file problem
Hi, For the simulation of a Protein ligand complex, i obtained the itp topology of the ligand from PRODRG 2 server and i ran the simulation of the complex a year back using GROMOS united atom force field by -ff gmx option in GROMACS 3.3 according to the Drg enzyme tutorial now i am unable to run the same protein ligand complex with the recent itp file obtained from the Current PRODRG server for the same ligand, i am getting error ATOM type CR1 not found in GROMACS 4.0.5. I am sure version of gromacs doesnt create any problem. Also i am getting atom mismatch error if i change the ATOM type to CR61, and i completely checked this number of atoms mismatch is only due to the .itp file included in prt.top. Thanks to justin for saying me about the problems in PRODRG topology, and suggesting to do improvements in the topology file for GROMOS force field, But i am totally confused how to edit the itp file. Before i used to include .itp file in .top file and add the residue number as DRG 1. now how to edit the .itp file, Somebody please help me -- -- * **Keep Enjoying !!!* *Yours Sincerely,* *B. Sarath Kumar, M.S (By Research), Tissue Culture and Drug Discovery Lab, Centre for Biotechnology, Anna University, Chennai.* -- 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] What is the autocorrelation time
Dear users: Let us say that I used g_analyze -g -fitfn exp and obtained the exponential autocorrelation time of a dataset. What does the exponential autocorrelation time represent? I imagine that it might be the time required to, on average, obtain a statistically independent sample, or perhaps the time required to obtain a 50% chance of the next sample being statistically independent. I've looked around the web and while I can find lots of information about how to obtain the exponential autocorrelation time, I am still unsure exactly what it represents. Thank you, Chris. -- 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] mixing Urey-Bradley and armonic in the same rtp file
Dear gromacs users, I am trying to port in gromacs the CHARMM36 all-atom carbohydrate force field. I downloaded the charmm files toppar_carb_apr12.tgz from http://mackerell.umaryland.edu/CHARMM_ff_params.html and I converted bonded and nonbonded parameters in gromacs format through the script convert_charmm_to_gromacs.pl. I have successfully generated the .top, using pdb2gmx, as well. But when I run grompp, it complains with errors like: *No default Angle types * * * and *No default Improper Dih. types* Look at the attacched file for the complete output from grompp. Now I inspected the missed interaction and, at least for the angle part, I figured out the problem. In the original charm parametrization there are angles parametrized as armonic and other angles parametrized as Urey-Bradley. Moreover, as far as I know, in the rtp file only one form can be used because of the [ bondedtypes ] clause. So my question is: Is there any way to mix, in the same residue (and hopefully in the same .rtp file), angles parametrized in the armonic form and Urey-Bradley parametrized angles? Is a correct solution parametrizing everything as armonic angles and mimic the bond potential between atom 1 and 3 present Urey-Bradley as a bond with same strenght and force value? Francesco grompp10.log Description: Binary 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] user defined potential(repulsive) for atoms falling with in three residues
Hi all, I am using a user defined potential to describe non-bonded interactions, which describes attractive potential for residues separated by four or more bonds . Now I want to describe a user defined potential(repulsive) for atoms falling with in three residues and which are not determined to be attractive, as I tried to elaborate below: condition 1: if the two atoms are separated by four or more bonds i use attractive LJ potential. condition 2: if two atoms are not determined to be attractive or fall with in three bonds of each other(i, i+3) then their interaction is defined by repulsive term: E(rep)= epsilon (sigma/rij)^12 Please let me know how I can implement this in Gromacs. Thanks and Regards, Mohan -- 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] itp file problem
On 5/16/12 2:25 PM, Sarath Kumar Baskaran wrote: Hi, For the simulation of a Protein ligand complex, i obtained the itp topology of the ligand from PRODRG 2 server and i ran the simulation of the complex a year back using GROMOS united atom force field by -ff gmx option in GROMACS 3.3 according to the Drg enzyme tutorial now i am unable to run the same protein ligand complex with the recent itp file obtained from the Current PRODRG server for the same ligand, i am getting error ATOM type CR1 not found in GROMACS 4.0.5. I am sure version of gromacs doesnt create any problem. Also i am getting atom mismatch error if i change the ATOM type to CR61, and i completely checked this number of atoms mismatch is only due to the .itp file included in prt.top. Thanks to justin for saying me about the problems in PRODRG topology, and suggesting to do improvements in the topology file for GROMOS force field, But i am totally confused how to edit the itp file. Before i used to include .itp file in .top file and add the residue number as DRG 1. now how to edit the .itp file, Somebody please help me The newer version of the PRODRG server is compatible with Gromos96 43a1, not the old ffgmx, which was a variant of Gromos87. Using 43a1 should solve the problem. -Justin -- Justin A. Lemkul, Ph.D. 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
[gmx-users] What is the autocorrelation time
Hi Chris, Probably these links give you simple and clear response for your question http://idlastro.gsfc.nasa.gov/idl_html_help/Time-Series_Analysis.html and http://www.statsoft.com/textbook/time-series-analysis/ HTH Stephane -- 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] Coupling Molecule type in *mdp file for Free Energy Simulation
Hello, I want to calculate the pKa shift of a buried aspartic acid residue in my protein using alchemical free energy perturbation. I do not know how to represent the individual aspartic acid attached to the protein in the required couple-moltype entry of the *mdp file. Any suggestions would be much appreciated. Cheers, Jackson Chief Elk Graduate Student The University of Montana Biophysics and Biochemistry -- 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] What is the autocorrelation time
Thank you Stephane. Unfortunately, neither of those links contains the information that I am seeking. Those links contain some example plots of autocorrelation functions including a discussion of time-spans over which the example time-series is autocorrelated and when it is not, but neither link defines the (exponential or integral) autocorrelation time except to show a plot and indicate when it is non-zero and when it fluctuates about zero. For example, I already know that the autocorrelation time describes the exponential decay of the correlation and that two values drawn from the same simulation are statistically independent if they are separated by a sufficient number of (accurate) autocorrelation times, but this information is not exactly a definition of the autocorrelation time. I am hoping to find a definition of the autocorrelation time in terms of the probability of drawing uncorrelated samples, although any complete definition will do. If anybody else has the time, I would appreciate it. Thank you, Chris. -- original message -- Probably these links give you simple and clear response for your question http://idlastro.gsfc.nasa.gov/idl_html_help/Time-Series_Analysis.html and http://www.statsoft.com/textbook/time-series-analysis/ HTH Stephane -- 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] constranit distance for pulling code
Dear gmxers, I have prepared the inputs and tried to run constraint distance pulling on two-molecule pair. However, one error is output which indicates that two atoms on the molecule including the pull group are beyond the 1-4 table range. I have chosen one reference group and one pull group. And both groups are parts of whole molecules. I find that no error is given when only pull opinions are commented out. So I guess this error can be caused by the pull code, i.e., the pull group is suddently moved to the distance defined by pull_init1, but the rest of molecule is not moved a bit, which leads to one much bigger 1-4 distance. Is it right? Cannot the pull code deal with the two groups belonging to only parts of two molecules? Please give me some hints, thanks a lot. Chaofu Wu -- Department of Chemistry and Materials Science Hunan University of Humanities, Science and Technology, Loudi 417000, the People's Republic of China (P.R. China)-- 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] constranit distance for pulling code
On 5/16/12 6:50 PM, xiaowu759 wrote: Dear gmxers, I have prepared the inputs and tried to run constraint distance pulling on two-molecule pair. However, one error is output which indicates that two atoms on the molecule including the pull group are beyond the 1-4 table range. I have I'm assuming you're seeing something like: http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-offhttp://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings Please always copy and paste the exact error message. chosen one reference group and one pull group. And both groups are parts of whole molecules. I find that no error is given when only pull opinions are commented out. So I guess this error can be caused by the pull code, i.e., the pull group is suddently moved to the distance defined by pull_init1, but the rest of molecule is not moved a bit, which leads to one much bigger 1-4 distance. Is it right? Cannot the pull code deal with the two groups belonging to only parts of two molecules? Please give me some hints, thanks a lot. The problem is that you're asking the pull code to do something that is physically unreasonable. Your assessment regarding the pull_init1 value is correct - you're asking the pull code to immediate constrain the intramolecular distance to some target, and it cannot do it. If you wish to pull the molecule apart (as in unfolding a protein), you'll have to modify your pull settings, as such a process certainly can be carried out. In the absence of actually seeing what your settings are, that's the best I can offer. -Justin -- Justin A. Lemkul, Ph.D. 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: Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks.
Thanks. I think I should have a look at some specific documents to understand the flow of control. Namely, to understand what is purpose of the subroutines in src/mdlib/. But I could not find such information in the Gromacs user manual. Do anyone know such an document? Thanks. kevin.len From: Mark Abraham Date: 2012-05-16 13:57 To: Discussion list for GROMACS users Subject: Re: [gmx-users] What is the subroutine for SHAKE or RATTLE? Thanks. On 16/05/2012 12:28 PM, kevin wrote: Hi, everyone. It is my first use of Gromacs and I am looking for a numerical scheme for one specific constrained SDE, the constrain is a macroscopic one, i.e., overdamped Langevin(Brownian dynamics) equations with an equality constraint which is expressed in form of expectation(or moment of n-th order). This is unlike the common 'micro' constraint(simply function in terms of variable in SDE) . I can not find such a subrountine for solving constrained SDE in MD codes in Gromacs. I see there is an algorithm called SHAKE or RATTLE which and it seems they could implement Langevin(or Brownian) dynamics with constraints. If convenient, could anyone help to point out which subroutine is specific for implementing SHAKE/RATTLE? Thanks in advance. Various files in src/mdlib/ deal with these kinds of algorithms. 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] Pressure at constant volume
Hello everyone, I am trying to estimate the thermodynamic expression, dP/dw at constant V and T, for my polymer-solvent system. Where P is the pressure, w is the mass fraction, V volume and T temperature. I guess this task can not be done by MD, as for constant Volume, pressure is meaningless. Since what g_energy reports is not the actual pressure which corresponds to that fixed Volume. Am I correct? (I mean building different binary systems with different mass fractions of w, and measuring average P (dP/dw) while keeping T and V constant does not produce meaningful results by MD) Please comment if this makes sense in MD or not. Thanks, J. -- 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] Spherical shaped box
Dear Tsjerk Thank you Sogol From: Tsjerk Wassenaar tsje...@gmail.com To: Kowsar Bagherzadeh kw_bagherza...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, May 16, 2012 2:46 PM Subject: Re: [gmx-users] Spherical shaped box Hi Sogol, You remove jumps over periodic boundary conditions, giving a continuous trajectory. That gives you a very nice view on diffusion in your system, which happens to be equal in all directions. Hence, the end result looks spherical. But that's not the same as having a spherical box. If you draw the box in VMD or Pymol, you'll see it's still close to the original (triclinic) shape, but has become a bit small in relation to your molecules. Cheers, Tsjerk On Wed, May 16, 2012 at 11:49 AM, Kowsar Bagherzadeh kw_bagherza...@yahoo.com wrote: Dear users, I am doing Protein Ligand simulation, increasing temp. from 100, 200, to 300 K. after 1ns of simulation in 300 K, the protein jumps out of the box and when I use the command trjconv_mpi -f *.trr -s *.tpr -o *new.trr -pbc nojump followed by trjconv_mpi -f new*.trr -s *.tpr -o new*.pdb -dump 1000 the box shape changes from dodecahedron to spherical. In Gromacs manual I read ; There are several possible shapes for space-filling unit cells. Some, as the rhombic dodecahedron and the truncated octahedron approach a spherical shape better than a cubic box and are therefore more economical for studying an (approximately spherical) macromolecule in solution, since less solvent molecules are required to fill the box given a minimum distance between macromolecular images... . Does it mean that it is ok and I can continue the simulation or I have to increase the box size? After simulation in 200 K the protein juped out of the box but using the same command the problem was fixed, without changing the box shape. Thank you in advance for the help Sogol -- gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands-- 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] Index selection in g_potential
Hi, if you want to calculate the potential of some groups (0, 3, 11), using make_ndx to creat a new group consisting of these groups. Then running g_potential. Cuong 2012/5/16 Andrew DeYoung adeyo...@andrew.cmu.edu Hi, I am using the utility g_potential. It takes (among other files) an index file. At the beginning of the run, it prompts me for a selection from the index file. Is it possible to make more than one selection, such that the potential is calculated for each selection, _separately_? If I enter something like this: 0 3 11 The output seems to only include the potential due to the first selection (0) and seems to ignore the others. Thanks for your time! Andrew DeYoung Carnegie Mellon University -- 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] nvt equilibration output
Respected sir, thanks for your kind reply... i applied position restrain during nvt step sir.. Thanking you, -- 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
