[gmx-users] (no subject)
Dear sir, i'm a new user of gromacs.i've done the installation correctly.while simulating my protein i encounter some of the problems.please give me ur suggetions or any reference to overcome this problem.this is my first experience of running the gromacs.kindly look for my problems and answer me as soon as possible.Thanks in advancesome of the errors are.. 1..while running pdb2gmx warning :'FE2' not found in residue topology database,trying to use 'FE'.i know that i've to use PRODGR to construct topology for Fe.but i'm not familiar to use it.please tell me the procedure of using it. 2..when i'm trying to run grompp Note: System has non-zero total charge : -6.02e+00.is it necessary to neutralise the charge, if so genion has to run Na means how much i've to add..ie how to calculate it... 3..with the avialable output file i tried to run mdrun.. showing the error that can not open File toplo.tpr but my tpr file is out3.tpr.i'm giving correctly in command also like mdrun -s out3 -o out4 -c out4 -v..plz give me ur advice to overcome. i'll be helpful if i get the answers.. thanking you, lali _ Who will win Bollywoods most coveted IIFA awards? You decide! Cast your vote! http://server1.msn.co.in/sp06/IIFA2006/static/weekend.asp ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
lalitha selvam wrote: Dear sir, i'm a new user of gromacs.i've done the installation correctly.while simulating my protein i encounter some of the problems.please give me ur suggetions or any reference to overcome this problem.this is my first experience of running the gromacs.kindly look for my problems and answer me as soon as possible.Thanks in advancesome of the errors are.. 1..while running pdb2gmx warning :'FE2' not found in residue topology database,trying to use 'FE'.i know that i've to use PRODGR to construct topology for Fe.but i'm not familiar to use it.please tell me the procedure of using it. You need to describe better what you're trying to do with an iron atom, and also which force field, for us to suggest a solution. This is not a help service for PRODRG, by the way, although some users will have some expertise with it. I can only suggest reading whatever documentation it provides. 2..when i'm trying to run grompp Note: System has non-zero total charge : -6.02e+00.is it necessary to neutralise the charge, if so genion has to run Na means how much i've to add..ie how to calculate it... Whether you want a neutral system depends what physical model you want to use. A physical Na+ ion will have +1e charge. I'll leave it to you to work out how many Na+ you need to neutralise -6e :-) (don't worry about the tiny fraction). 3..with the avialable output file i tried to run mdrun.. showing the error that can not open File toplo.tpr but my tpr file is out3.tpr.i'm giving correctly in command also like mdrun -s out3 -o out4 -c out4 -v..plz give me ur advice to overcome. Most likely, you aren't giving the command you think you are :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
Your reported errors: 1..while running pdb2gmx warning :'FE2' not found in residue topology database... What force field are you using in pdb2gmx? look at that .itp file and the files that it includes (.itp file is prefaced by 'ff' and is in share/gromacs/top/ or similar directory) If you can't get pdb2gmx to work then get rid of your Iron from the PDB and run pdb2gmx to get the .gro and then add the iron back into the .gro (pdb2gmx seems to work easily only with pure protein files, although perhaps a more experienced user can get it to work with anything). Regardless, it is key to know what your force field is calling the iron2 atom. 2..when i'm trying to run grompp Note: System has non-zero total charge : -6.02e+00. is it necessary to neutralise the charge, if so genion has to run Na means how much i've to add..ie how to calculate it... You must have a charge neutral system to use Ewald/PME/etc... If you are using a pure cutoff or 2-step cutoff then a net negative charge should be fine (as long as your cutoff values are otherwise acceptable). I am not sure what your 2nd question is here??? Add 6 positive monovalent ions to neutralize. 3..with the avialable output file i tried to run mdrun.. showing the error that can not open File toplo.tpr but my tpr file is out3.tpr.i'm giving correctly in command also like mdrun -s out3 -o out4 -c out4 -v First of all, forget about mdrun until you solve the other problems. How do you run grompp successfully if you have problems with pdb2gmx? Regardless, try -s out3.tpr (add the .tpr) although I can't imagine that that will help. It appears that your -s argument is not getting read... look for errors/warning before the one that you mentioned. Hope that helps. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
[EMAIL PROTECTED] wrote: 2..when i'm trying to run grompp Note: System has non-zero total charge : -6.02e+00. is it necessary to neutralise the charge, if so genion has to run Na means how much i've to add..ie how to calculate it... You must have a charge neutral system to use Ewald/PME/etc... That's not true. There's nothing intrinsic about those treatments that prevents non-neutral systems... quite the contrary in fact, although I've seen this must-be-neutral view expressed on this list before. Further there is nothing in the gromacs 3.3 manual that suggests there is a gromacs constraint to have neutral systems, although I haven't ever wanted to try it out myself to see. Whether you'd want a non-neutral system for a given problem is a matter for the user to decide :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] New website
The site looks nice. My only difficulty is that I like to sit on the users mailing list and press the refresh button my my browser every few hours to see the new comments. That now takes me back to the The gmx-users Archives page. It's a tiny problem, but when one is hoping for an answer and refreshing often, it can become an annoyance. Seperately, How do I post a response that gets added to the thread of the initial comment? This is not a new problem for me. Currently, I copy the subject from the list and write a new email with the same subject (e.g. this one [gmx- users] New website) Thanks, Chris. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] New website
[EMAIL PROTECTED] wrote: The site looks nice. My only difficulty is that I like to sit on the users mailing list and press the refresh button my my browser every few hours to see the new comments. That now takes me back to the The gmx-users Archives page. It's a tiny problem, but when one is hoping for an answer and refreshing often, it can become an annoyance. Seperately, How do I post a response that gets added to the thread of the initial comment? This is not a new problem for me. Currently, I copy the subject from the list and write a new email with the same subject (e.g. this one [gmx- users] New website) Umm, I'd guess most of us just reply to the emails that get sent to subscribers. I can't think of another way to do it! Your solution of copy-and-paste-the-subject will not work with all list-management software - there is more behind-the-scenes header stuff that controls thread recognition than the subject line. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: [gmx-developers] smalloc.c
Yang Ye wrote:
David van der Spoel wrote:
Patricia Soto Becerra wrote:
Hi,
I want to implement the rest algorithm (PNAS, 102, 39, 13749-13754.
(2005)). I have been following the discussions in the list of a very
similar implementation, particularly:
http://www.gromacs.org/pipermail/gmx-developers/2006-January/001493.html
http://www.gromacs.org/pipermail/gmx-developers/2006-January/001494.html
Nevertheless, I get the error message:
__
Source code file: smalloc.c, line: 113
Fatal error:
calloc for ir-opts.nrdf (nelem=105789, elsize=4, file tpxio.c,
line 487)
---
I just cannot figure it out... Does anybody have a suggestion on how
to solve this?
there must be an inconsistency in your tpr file. Did you try to
modify that?
This mistake shall not be derived from the changes I suggested. This
is the changes I have made. They are declared to be under GPL.
include/types/idef.h
1. in first enumaddF_EPOT_NOSOLafter F_NRE
include/tgroup.h
2. extern void sum_epot_nosol(t_grpopts *opts,t_groups *grps,real
epot[]);
src/kernel/md.c
3. change snew(ener,F_NRE); to snew(ener,F_NRE+1);
4. replace
sum_epot((inputrec-opts),grps,ener);
to
sum_epot_nosol((inputrec-opts),grps,ener); /*Fill in F_EPOT_NOSOL*/
5. replace
if ((repl_ex_nst 0) (step 0) !bLastStep
do_per_step(step,repl_ex_nst))
bExchanged =
replica_exchange(log,mcr,repl_ex,state,ener[F_EPOT],step,t);
to
if ((repl_ex_nst 0) (step 0) !bLastStep
do_per_step(step,repl_ex_nst))
bExchanged =
replica_exchange(log,mcr,repl_ex,state,ener[F_EPOT_NOSOL],step,t);
/src/mdlib/tgroup.c
6. add
void sum_epot_nosol(t_grpopts *opts,t_groups *grps,real epot[])
{
int i;
sum_epot(opts,grps,epot);
epot[F_EPOT_NOSOL] = epot[F_EPOT] - \
(grps-estat.ee[egCOULSR][grps-estat.nn-1] + \
grps-estat.ee[egLJSR][grps-estat.nn-1] + \
grps-estat.ee[egLJ14][grps-estat.nn-1] + \
grps-estat.ee[egCOUL14][grps-estat.nn-1] + \
grps-estat.ee[egCOULLR][grps-estat.nn-1] + \
grps-estat.ee[egLJLR][grps-estat.nn-1] + \
grps-estat.ee[egBHAMSR][grps-estat.nn-1] + \
grps-estat.ee[egBHAMLR][grps-estat.nn-1]);
}
Regards,
Yang Ye
Forgot this: above code takes as granted that last temperature coupling
group is solvent. It doesn't take the caution to check the group's content.
Yang Ye
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Re: [gmx-users] New website
Hi Chris, On May 12, 2006, at 8:59 AM, [EMAIL PROTECTED] wrote: The site looks nice. My only difficulty is that I like to sit on the users mailing list and press the refresh button my my browser every few hours to see the new comments. That now takes me back to the The gmx-users Archives page. It's a tiny problem, but when one is hoping for an answer and refreshing often, it can become an annoyance. We'll try to fix that. In the mean time, you can access the list directly at http://www.gromacs.org/pipermail/gmx-users/ Seperately, How do I post a response that gets added to the thread of the initial comment? This is not a new problem for me. Currently, I copy the subject from the list and write a new email with the same subject (e.g. this one [gmx- users] New website) Mailman (just as most mail clients) actually keep track of threads through the Message-ID field in the header, and then replies will have a References field containing the Message ID of the parent (even if you change the subject!) Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] (no subject)
Hello gromacs users, My computer could not handle a file having size more than 2GB. But my XTC file is of 5GB.Hence i want to make this file in to small files having size less than 2GB and use them with analysing tools like g_rmsf.Kindly let me know whether it is possible to submit multiple input files(XTC) to the analysing tools of gromacs.Your help is deeply appreciated. Thanking you prasad reddy. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] (no subject)
prasad reddy wrote: Hello gromacs users, My computer could not handle a file having size more than 2GB. But my XTC file is of 5GB.Hence i want to make this file in to small files having size less than 2GB and use them with analysing tools like g_rmsf.Kindly let me know whether it is possible to submit multiple input files(XTC) to the analysing tools of gromacs.Your help is deeply appreciated. In general, no you can't submit multiple trajectory files and have them concatenated magically. Some utilities like trjcat will accept them, but only to write the concatenation, not to analyze it. Your options include hacking the source code of the utilities you want to use, getting a new file system, reducing the frequency of the data in the existing files using trjconv, not writing data so frequently during the simulation or using different analysis tools. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: topology transformation
Anthony Cruz wrote: Thank you for your answer. I find it to day searching the mailing list because I have some problems with the mail and I dont receive this mail. I try the beta version but I got confised because i dont see the GROMOS terminology ej. gb_x, ga_x ect. If I use the beta version i could use the file as I get it from PRODRG? or I need to change it??? I always created .rtp building blocks for my residues and converted the explicit PRODRG values to GROMOS nomenclature with the help of ffG43a1bon.itp. But it is also possible to use explicit values with 43A1, one of my students did it like this (PRODRG has some more angle types than standard 43A1). You may check with gmxdump if the resulting .tpr is OK. Regards Christian ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] About calculations of viscosity
Dear gmx-users, I’m a new GMX user. I notice from either the user-manual or the references (Palmer, PRE 49 359, B. Hess, JCP 116, 209, etc.) that there seem to be at least 3 methods available in Gromacs: Einstein relation, TCAF and periodic perturbation method. But I’m not very clear about how to set the calculations and how to get the according viscosity values. My understanding is this: For Einstein relation calculations, there is no special setting in the md.mdp file, and the viscosity value is gotten by the visco.xvg file generated by ‘g_energy �Cvis’; For TCAF, also there is no special setting in the md.mdp file, and the viscosity value is gotten by fitting the data of visco_k.xvg file generated by ‘g_tcaf’; For the periodic perturbation method, two NEMD items, a ‘accelerate’ value in X direction should be specified to all atoms and a ‘cos_acceleration’ value should be given, and the viscosity value is gotten from the ‘1/Viscosity(SI)’ item of the ‘g_energy’ results. I’m eager for any instructions about techniques on the calculations and the value ranges. Thanks. Zhao ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] New website
On May 12, 2006, at 12:52 PM, Yang Ye wrote: Erik Lindahl wrote: Hi Chris, On May 12, 2006, at 8:59 AM, [EMAIL PROTECTED] wrote: The site looks nice. My only difficulty is that I like to sit on the users mailing list and press the refresh button my my browser every few hours to see the new comments. That now takes me back to the The gmx-users Archives page. It's a tiny problem, but when one is hoping for an answer and refreshing often, it can become an annoyance. We'll try to fix that. In the mean time, you can access the list directly at http://www.gromacs.org/pipermail/gmx-users/ Some months, I have written to Eric to add our mailing list to Gmane.org. http://news.gmane.org/gmane.science.biology.gromacs.user It has a good web interface while many other access methods are provided. It is currently a closed mailing list but shall be used to post for members (but I failed to do so just now). Eric, would you like to check this out? Perhaps, you are already trying something. Not sure what you want me to check, but I haven't changed any list configurations lately. As for posting-requires-subscription, that's unfortunately necessary to avoid spam making it to the list. Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] pressure scaling.
i just removed the problem. the atoms were too close to each other. i
have increased the system size. moreover i used trjconv to center the
atoms. the solution was there in the previous posts. anyway thnx for
your help.
have a nice day!On 5/12/06, Gale, Ella [EMAIL PROTECTED] wrote:
I guess that because it's outside the box perhaps,
you have coordinates that are bigger than the box vectors, if gromacs
is clever enough to wrap it round they could overlap and overlapping
atoms (or atoms too close) can cause this. I posted a question about a
very similar problem yesterday.
Not sure if that will help.
Ella Gale
-Original Message-
From: [EMAIL PROTECTED] on behalf of karamyog singh
Sent: Fri 5/12/2006 2:16 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] pressure scaling.
hallo gromaxers, i am new to gromacs and i am facing another problem. I got
the following error when i tried to simulate a dilute gas. I tried removing
pbc but then the run hangs. i even tried changing my box vectors to satisfy
the triclinic conditions.
moreover when i view my initial structure using ngmx. the structure doesnt
lie in the box completely. its to the left. i think i need to change the
center of the box for that. am i right?
i have used arbit positions in the conf.gro file. Is this going to hamper my
run in any way? i believe since i am trying to simulate a gas, i can use
arbit positions. also i am using only 64 atoms. my co-ordinates are all
positive and less than 1(0.001 to 0.999). my box vectors are 1.920 1.870
1.655 0.000 0.000 0.950 0.000 0.950 0.800.
if any other detail is required please let me know.
how do i reduce pressure scaling? and how can i fix pbc for my cell?
-
karamyog.
-
ERROR :-
-
step 0
Step 1 Warning: pressure scaling more than 1%, mu: 8.68552e+18 8.68552e+18
8.68552e+18
Step 2 Warning: pressure scaling more than 1%, mu: 3.43938e+19 3.43938e+19
3.43938e+19
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[
0]={
nan,
nan, nan}
Box[
1]={
nan,
nan, nan}
Box[
2]={
nan,
nan, nan}
Can not fix pbc.
Warning: Only triclinic boxes with the first vector parallel to the x-axis
and the second vector in the xy-plane are supported.
Box (3x3):
Box[
0]={
nan,
nan, nan}
Box[
1]={
nan,
nan, nan}
Box[
2]={
nan,
nan, nan}
Can not fix pbc.
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]
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SV: [gmx-users] failing to constraint distance
Hello Gmx-users, can it be true that it is not possible to constrain the vector between 2 molecules defined as constrain group and reference group in a ppa file? After a longer struggle it seems to me that one can only constrain _one_ of the following: I. The length of the vector II.,III.,IV., The length of the vector onto the x, y, and z, coordinate axis, respectively. This means that setting: "constraint_direction = 0.0 1.0 1.0" or "constraint_direction = 1.0 1.0 1.0" in the ppa file will constrain _anything_! Why is that? Best regards -Soren Soren Enemark [EMAIL PROTECTED] skrev: Dear Gromacs users, I have difficulties to get the distance between two molecules constraint using a .ppa file as described in Chapter 6 in the manual. I tried to combine the different options in almost all ways but nothing seems to constraint the distance. To check that the inter molecular distance is unchanged I useg_dist. Is it unprecise? Can the inter molecular constraint be used together with the normal bond/angle constraints set in the mdp file, or are they somehow working against each other? I include a test md.mdp file, my constraint.ppa file and a piece of the dist.xvg file generated with g_dist md.mdp --- title = FWS integrator = mddt = 0.001nsteps = 2000 ; 2 psns_type = grid pbc = xyznstlist = 1rlist = 1.1 nstxout = 10nstvout = 10nstfout = 10nstlog = 10nstenergy = 10nstxtcout = 0energygrps = Complex_A Complex_B comm_mode = Linearnstcomm = 1comm_grps = Complex_All coulombtype = PMEoptimize_fft = yesfourierspacing = 0.12pme_order = 4rcoulomb = 1.1vdwtype = Switchrvdw_switch = 1.1rvdw = 1.2 tcoupl = berendsentc_grps = Complex_All SOL_NA+tau_t = 0.1 0.1ref_t = 300 300 pcoupl = berendsenpcoupltype = isotropictau_p = 5compressibility = 4.5e-5ref_p = 1.1 gen_vel = nogen_temp = 300genseed = 42 ;constraints = hbonds;constraint_algorithm = lincs;unconstrained_start = noconstraint.ppa verbose = yesruntype = constraintgroup_1 = Complex_Areference_group = Complex_B;reftype = com_t0;reflag = 1pulldim = Y Y Yconstraint_direction = 1.0 1.0 1.0;constraint_tolerance = 0.010dist.xvg # This file was created Fri Apr 21 10:37:52 2006# by the following command:# g_dist -f traj.trr -s topol.tpr -n index.ndx -o dist.xvg## g_dist is part of G R O M A C S:## God Rules Over Mankind, Animals, Cosmos and Such#@ title "Distance"@ xaxis label "Time (ps)"@ yaxis label "Distance (nm)"@TYPE xy@ view 0.15, 0.15, 0.75, 0.85@ legend on@ legend box on@ legend loctype view@ legend 0.78, 0.8@ legend length 2@ s0 legend "|d|"@ s1 legend "d\sx\N"@ s2 legend "d\sy\N"@ s3 legend "d\sz\N" 0.000 4.39150 4.39143 -0.00756 0.02317 0.010 4.39139 4.39132 -0.00756 0.02328 0.020 4.39129 4.39122 -0.00755 0.02338 0.030 4.39119 4.39112 -0.00756 0.02349 0.040 4.39110 4.39103 -0.00759 0.02360 0.050 4.39102 4.39095 -0.00763 0.02372 0.060 4.39094 4.39087 -0.00767 0.02384 0.070 4.39086 4.39079 -0.00770 0.02395 0.080 4.39079 4.39071 -0.00772 0.02405 0.090 4.39071 4.39063 -0.00773 0.02414 0.100 4.39062 4.39054 -0.00774 0.02424 0.110 4.39052 4.39044 -0.00775 0.02435 0.120 4.39042 4.39034 -0.00778 0.02448.. 0.900 4.38858 4.38848 -0.00831 0.02686 0.910 4.38866 4.38857 -0.00831 0.02677 0.920 4.38875 4.38866 -0.00830 0.02668 0.930 4.38883 4.38874 -0.00828 0.02658 0.940 4.38890 4.38881 -0.00826 0.02649 0.950 4.38898 4.38889 -0.00824 0.02639 .. 1.930 4.39870 4.39867 -0.00592 0.01429 1.940 4.39872 4.39870 -0.00591 0.01425 1.950 4.39874 4.39871 -0.00589 0.01422 1.960 4.39874 4.39871 -0.00586 0.01419 1.970 4.39874 4.39871 -0.00584 0.01417 1.980 4.39874 4.39872 -0.00581 0.01413 1.990 4.39876 4.39874 -0.00577 0.01408 2.000 4.39880 4.39878 -0.00575 0.01401Finding the max and min distance shows that the molecules move 0.1 Ång over a period of 1 ps. I am simply demanding too much from the program, since each of the molecules are about 450 aa?Can U plz help me to solve this problem! I also have one question to the constraint-direction, if I set this to "0 0 0" then what do I constraint??Thanks, Soren___gmx-users mailing listgmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED]Can't post? Read http://www.gromacs.org/mailing_lists/users.php___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Re: angle restraints
Maarten, So you are saying that lambda is just controlling the restraints and nothing else? That is, you are using lambda-dependent angle restraints? If this is the case, the problem is the fix for the bug that I referred you, as implemented in 3.3.1. From the bugzilla page, here's the fix: This was a nasty bug. The problem was that the angle-restraint parameters were stored incorrectly in the tpr file. I have fixed it completely in the CVS. I also made a fix for 3.3.1, but there the B-state parameters are always copied from the A-state. In other words, in 3.3.1, the claim is that angle restraint parameters can't be made to be lambda-dependent; B state and A state parameters are the same. I am confused why you would be getting a nonzero dv/dlambda at all in this case. According to Berk, the angle restraints have the correct lambda dependence in the CVS version. So if you are really intent on doing things this way (that is, using lambda-dependent angle restraints) you may want the CVS version. Alternatively, you can do what I do, which is run simulations using normal (non-lambda dependent) angle restraints with a bunch of different spring constants, rather than using the free energy code. Think of the spring constant like lambda. Then dV/dlambda=d(restraint energy)/dK, where K is the spring constant. For harmonic restraints, this is (restraint energy)/K. So you can compute dV/dlambda yourself from the energies that are output by just taking the angle restraint energy and dividing by the spring constant. Again, I'm still not clear that this is exactly what you're trying to do. As far as I can tell if your only lambda dependence is in the angle restraints, and you are using 3.3.1, you should be getting a dv/dlambda that is zero everywhere, unless you've done something strange like turning on soft core potentials or something. David On 5/11/06, Maarten Wolf [EMAIL PROTECTED] wrote: David, Thanks for your reply. I am currently using 3.3.1 code. I am increase the force, to be able to calculate the free energy required of introducing the angle restraints in the system. I use small force increments each run, using a delta_lambda of 0. Decreasing or increasing in my view only changes the sign of the overall graph, but it should not allow dG/dl to cross zero. Thanks, Maarten From: David Mobley [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Date: Thu, 11 May 2006 09:34:28 -0700 Subject: Re: [gmx-users] angle restraints Maarten, What version of the code are you using? There was a bug in the angle restraints code until 3.3.1 (or 3.3 cvs) which caused angle restraints to turn off gradually as a function of lambda in free energy calculations, if I remember correctly. (See bugzilla for details: http://bugzilla.gromacs.org/show_bug.cgi?id=43). However, I'm not sure that relates to the problem you're describing, but it probably does, depending on the version you are using. What exactly are you changing in the free energy calculation? Are you changing the angle restraint as a function of lambda? If so, which way are you changing it? Decreasing or increasing restraints? David On 5/11/06, Maarten Wolf [EMAIL PROTECTED] wrote: Dear users, I have a small system with a number of small peptides. I want to constraint the angle between the N-term to C-term vectors of different peptides. This works well, but if I do a FEP calculation the dG/dl becomes smaller than zero at some point. I expected it to be at least allways greater than zero (zero in the limit that the restraint does not have to do anything), since a force has to be aplied to restraint the angles. Can anybody explain where I am going wrong? Thanks Maarten Send instant messages to your online friends http://uk.messenger.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users MvG Maarten ** ** Work Adress Julianalaan 136 ** ** 2628 BL Delft ** ** Netherlands ** ** +31(0)15-2789382** ** ___ Switch an email account to Yahoo! Mail, you could win FIFA World Cup tickets. http://uk.mail.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't
[gmx-users] N-terminal and C-terminal modifications
What is the best approach to handle N and C-terminal modifications (e.g. formylation, chemical modification)? Is it better to define custom residue types or to adjust the termini database? Thanks in advance for your advice. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] question about freezing a group
Dear gromacs users, I'm doing a MD simulation of protein in water. I freeze an atom in z direction, e.g. freezdim N N Y, and afm pull another atom along -z direction, e.g. afm_dir = 0 0 -1 afm_rate1 = 0.01 afm_init1 equals the coordinate of the pulled atom. After about 200ps simulation, I found that the z coordinate of the pulled atom dropped with string, however the z coordinate of the frozen atom also dropped alot. I think z of the frozen atom should be constant, but why it drops? Waiting for your help. Thanks a lot! Linchen Gong ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] question about trjconv
Dear gromacs users, I have another question concerning about trjconv. Is anyway to make trjconv uninteractive, e.g. do not have to choose selected group to output or fit interactively. Since I'm using gromacs in a cluster and must bsub jobs to queue, I don't know how to handle interactive option. Thanks a lot！ Linchen Gong ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
