Dear Mark,<div><br></div><div>Thank you very much for the reply.</div><div>To clarify , I have asked all the warning based questions to get acknowledged with your expert opinion, apart from the manual based view.</div><div>
According to your suggestion NPT with Position restraints is messy,but still I have seen lots of manual/tutorial (including Bevans Lab ) suggesting the position restraining of protein during NVT as well as NPT. That is the reason I have followed the same. Please clarify your view on this matter. </div>
<div><br></div><div>Thak you very much in advance.</div><div> </div><div><br clear="all"><div>Pavan Payghan</div>
<div> </div>
<div> </div>
<div> </div><br>
<br><br><div class="gmail_quote">On Thu, Jun 7, 2012 at 4:58 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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Today's Topics:<br>
<br>
1. Re: Warnings related to Berendsen pressure coupling and use<br>
the refcoord_scaling option (Mark Abraham)<br>
2. Re: GPU crashes (Justin A. Lemkul)<br>
3. Re: Re: change in rename of 1POPC to 1LIG though coordinate<br>
and atom same in 1LIG of 1POPC, during solvation of system<br>
(Justin A. Lemkul)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 07 Jun 2012 20:42:47 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] Warnings related to Berendsen pressure<br>
coupling and use the refcoord_scaling option<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4FD085A7.5000403@anu.edu.au" target="_blank">4FD085A7.5000403@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 7/06/2012 8:33 PM, PAVAN PAYGHAN wrote:<br>
><br>
><br>
> Dear Gromacs Users,<br>
><br>
> I am using gromacs version 4.5.5.and running my jobs on single<br>
> node with 8 cores. My system contains about 425000 atoms (protein +<br>
> Lipid +SOL). I have successfully reached up to Energy minimization<br>
> step.As per the suggestion by Dear Mark, I am starting my NPT<br>
> equilibration with Berendsen and further with Parinello-Rahman to get<br>
> the right ensemble.But when I am trying for NPT equilibration with<br>
> Berendsen, getting following Warnings.<br>
><br>
> WARNING 1 [file npt.mdp]: Using Berendsen pressure coupling<br>
> invalidates the true ensemble for the thermostat<br>
><br>
> WARNING 2 [file npt.mdp]: You are using pressure coupling with<br>
> absolute position restraints, this will give artifacts. Use the<br>
> refcoord_scaling option.<br>
><br>
> And about 10 such LINCS warnings while running the job as shown below:<br>
><br>
> Step 39, time 0.078 (ps)LINCS WARNING<br>
><br>
> relative constraint deviation after LINCS:<br>
><br>
> rms 0.000029, max 0.000473 (between atoms 890 and 891)<br>
> bonds that rotated more than 30 degrees:<br>
> atom 1 atom 2 angle previous, current, constraint length<br>
> 12050 12049 31.2 0.1000 0.1000 0.1000<br>
> 11721 11720 46.0 0.1000 0.1000 0.1000<br>
> 5496 5495 36.8 0.1000 0.1000 0.1000<br>
><br>
> With --maxwarn option I am able to run it, and output density and<br>
> pressure seems perfectly alright.<br>
><br>
> Based on the same I want to know:-<br>
><br>
> 1. How does pressure coupling with Berendsen invalidates the true<br>
> ensemble?<br>
><br>
<br>
See manual sections for T and P coupling for introductory discussion.<br>
<br>
> At least for initial fixing of density and pressure?<br>
><br>
> Whether to bother for above mentioned warning or ignore it?<br>
><br>
<br>
Since you're going to do more equilibration after this, you be the judge.<br>
<br>
> 2. Pressure coupling with absolute position restraints warning how it<br>
> will lead to artifacts?<br>
><br>
> How one can use refcoord_scaling option in this situation?<br>
><br>
<br>
See manual.<br>
<br>
> Whether to bother for above mentioned warning or ignore it?<br>
><br>
<br>
Position restraints and NPT is messy. Choose your poison.<br>
<br>
> 3. Using Berendsen with semiisotropic couple type is wrong method or<br>
> no such problem?<br>
><br>
> Please suggest me whether to move ahead with ignorance to the warnings<br>
> or to change some parameters in mdp file?<br>
><br>
<br>
That's your judgement to make. How does your preparation protocol<br>
compare to the ones you have read about in the recent literature?<br>
<br>
Mark<br>
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Message: 2<br>
Date: Thu, 07 Jun 2012 07:25:31 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] GPU crashes<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4FD08FAB.5000004@vt.edu" target="_blank">4FD08FAB.5000004@vt.edu</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
<br>
<br>
On 6/7/12 3:57 AM, lloyd riggs wrote:<br>
> Did you play with the time step? Just currious, but I woundered what<br>
> happened with 0.0008, 0.0005, 0.0002. I found if I had a good behaving<br>
> protein, as soon as I added a small (non-protein) molecule which rotated<br>
> wildly while attached to the protein, it would crash unless I reduced the<br>
> time step to the above when constraints were removed after EQ ... always it<br>
> seemed to me it didnt like the rotation or bond angles, seeing them as a<br>
> violation but acted like it was an amino acid? (the same bond type but with<br>
> wider rotation as one end wasnt fixed to a chain) If your loop moves via<br>
> backbone, the calculated angles, bonds or whatever might appear to the<br>
> computer to be violating the parameter settings for problems, errors, etc as<br>
> it cant track them fast enough over the time step. Ie atom 1-2-3 and then<br>
> delta 1-2-3 with xyz parameters, but then the particular set has additional<br>
> rotation, etc and may include the chain atoms which bend wildly (n-Ca-Cb-Cg<br>
> maybe a dihedral) but proba! bly not this.<br>
><br>
> Just a thought but probably not the right answere as well, it might be the<br>
> way it is broken down (above) over GPUs, which convert everything to<br>
> matricies (non-standard just for basic math operations not real matricies per<br>
> say) for exicution and then some library problem which would not account for<br>
> long range rapid (0.0005) movements at the chain (Ca,N,O to something else)<br>
> and then tries to apply these to Cb-Cg-O-H, etc using the initial points<br>
> while looking at the parameters for say a single amino acid...Maybe the<br>
> constraints would cause this, which would make it a pain to EQ, but this<br>
> allowed me to increase the time step, but would ruin the experiment I had<br>
> worked on as I needed it unconstrained to show it didnt float away when<br>
> proteins were pulled, etc...I was using a different integrator though...just<br>
> normal MD.<br>
><br>
<br>
I have long wondered if constraints were properly handled by the OpenMM library.<br>
I am constraining all bonds, so in principle, dt of 0.002 should not be a<br>
problem. The note printed indicates that the constraint algorithm is changed<br>
from the one selected (LINCS) to whatever OpenMM uses (SHAKE and a few others in<br>
combination). Perhaps I can try running without constraints and a reduced dt,<br>
but I'd like to avoid it.<br>
<br>
I wish I could efficiently test to see if this behavior was GPU-specific, but<br>
unfortunately the non-GPU implementation of the implicit code can currently only<br>
be run in serial or on 2 CPU due to an existing bug. I can certainly test it,<br>
but due to the large number of atoms, it will take several days to even approach<br>
1 ns.<br>
<br>
> ANd your cutoffs for vdw, etc...Why are they 0? I dont know if this means a<br>
> defautl set is then used...but if not ? Wouldnt they try integrating using<br>
> both types of formula, or would it be just using coulumb or vice versa? (dont<br>
> know what that would do to the code but assume it means no vdw, and all<br>
> coulumb but then zeros are alwyas a problem for computers).<br>
><br>
<br>
The setup is for the all-vs-all kernels. Setting cutoffs equal to zero and<br>
using a fixed neighbor list triggers these special optimized kernels. I have<br>
also noticed that long, finite cutoffs (on the order of 4.0 nm) lead to<br>
unacceptable energy drift and structural instability in well-behaved systems<br>
(even the benchmarks). For instance, the backbone RMSD of lysozyme is twice as<br>
large in the case of a 4.0-nm cutoff relative to the all-vs-all setup, and the<br>
energy drift is quite substantial.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 07 Jun 2012 07:27:54 -0400<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Re: change in rename of 1POPC to 1LIG though<br>
coordinate and atom same in 1LIG of 1POPC, during solvation of system<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4FD0903A.5080603@vt.edu" target="_blank">4FD0903A.5080603@vt.edu</a>><br>
Content-Type: text/plain; charset=UTF-8; format=flowed<br>
<br>
<br>
<br>
On 6/6/12 1:12 PM, Sangita Kachhap wrote:<br>
><br>
>> Send gmx-users mailing list submissions to<br>
>> <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
>><br>
>> To subscribe or unsubscribe via the World Wide Web, visit<br>
>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>> or, via email, send a message with subject or body 'help' to<br>
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>><br>
>> When replying, please edit your Subject line so it is more specific<br>
>> than "Re: Contents of gmx-users digest..."<br>
>><br>
>><br>
>> Today's Topics:<br>
>><br>
>> 1. Re: Re: change in rename of 1POPC to 1LIG though coordinate<br>
>> and atom same in 1LIG of 1POPC, during solvation of system<br>
>> (Justin A. Lemkul)<br>
>> 2. Segmentation fault - pdb2gmx specbond.dat (Steven Neumann)<br>
>> 3. energy conservation: shift vs shifted user potential<br>
>> (Anja Kuhnhold)<br>
>> 4. Cannot get correct pressure value with MTTK pressure coupling<br>
>> (Bao Kai)<br>
>> 5. Re: Cannot get correct pressure value with MTTK pressure<br>
>> coupling (Justin A. Lemkul)<br>
>><br>
>><br>
>> ----------------------------------------------------------------------<br>
>><br>
>> Message: 1<br>
>> Date: Wed, 06 Jun 2012 08:56:04 -0400<br>
>> From: "Justin A. Lemkul"<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
>> Subject: Re: [gmx-users] Re: change in rename of 1POPC to 1LIG though<br>
>> coordinate and atom same in 1LIG of 1POPC, during solvation of system<br>
>> To: Discussion list for GROMACS users<<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
>> Message-ID:<<a href="mailto:4FCF5364.800@vt.edu" target="_blank">4FCF5364.800@vt.edu</a>><br>
>> Content-Type: text/plain; charset=UTF-8; format=flowed<br>
>><br>
>><br>
>><br>
>> On 6/6/12 8:52 AM, Sangita Kachhap wrote:<br>
>><br>
>>>> On 6/6/12 3:09 AM, Sangita Kachhap wrote:<br>
>>>>><br>
>>>>> Hello all<br>
>>>>> I have to do MD simulation of membrane protein having docked ligand in POPC<br>
>>>>> lipid bilayer.<br>
>>>>> I am geeting error during solvation of system:<br>
>>>>> Resname of 1POPC in system_shrink1.gro converted into 1LIG<br>
>>>>><br>
>>>>><br>
>>>>> I have done following:<br>
>>>>><br>
>>>>> GROMACS COMMAND<br>
>>>>><br>
>>>>> 1) Generate topol.top using GROMOS96 53A6 parameter set<br>
>>>>> pdb2gmx -f 3gd8-mod.pdb -o 3gd8-mod-processed.gro -water spc<br>
>>>>><br>
>>>>><br>
>>>>> at prompt select 14<br>
>>>>><br>
>>>>> 2) Download:<br>
>>>>> * popc128.pdb - the structure of a 128-lipid POPC bilayer<br>
>>>>> * popc.itp - the moleculetype definition for POPC<br>
>>>>> * lipid.itp - Berger lipid parameters<br>
>>>>><br>
>>>>> from <a href="http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies" target="_blank">http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies</a><br>
>>>>><br>
>>>>> 3) Modify topol.top with:<br>
>>>>> #include "gromos53a6.ff/forcefield.itp"<br>
>>>>><br>
>>>>> to:<br>
>>>>><br>
>>>>> #include "gromos53a6_lipid.ff/forcefield.itp"<br>
>>>>><br>
>>>>><br>
>>>>> &<br>
>>>>><br>
>>>>> ; Include Position restraint file<br>
>>>>> #ifdef POSRES<br>
>>>>> #include "posre.itp"<br>
>>>>> #endif<br>
>>>>> ; Include ligand topology<br>
>>>>> #include "ligand-full.itp"<br>
>>>>><br>
>>>>> ; Include POPC chain topology<br>
>>>>> #include "popc.itp"<br>
>>>>><br>
>>>>> ; Include water topology<br>
>>>>> #include "gromos53a6_lipid.ff/spc.itp"<br>
>>>>><br>
>>>>> and at the end add LIG 1 in [molecules]<br>
>>>>><br>
>>>>> 4) cp files<br>
>>>>> aminoacids.rtp<br>
>>>>> aminoacids.hdb<br>
>>>>> aminoacids.c.tdb<br>
>>>>> aminoacids.n.tdb<br>
>>>>> aminoacids.r2b<br>
>>>>> aminoacids.vsd<br>
>>>>> ff_dum.itp<br>
>>>>> ffnonbonded.itp<br>
>>>>> ffbonded.itp<br>
>>>>> forcefield.itp<br>
>>>>> ions.itp<br>
>>>>> spc.itp<br>
>>>>> watermodels.dat<br>
>>>>><br>
>>>>> from gromacs top to directory named gromos53a6_lipid.ff in working<br>
>>>>> directory.<br>
>>>>> Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes ])from<br>
>>>>> lipid.itp to ffnonbonded.itp& ffbonded.itp and create a forcefield.doc<br>
>>>>> file<br>
>>>>> that contains a description of the force field parameters contain "GROMOS96<br>
>>>>> 53A6<br>
>>>>> force field, extended to include Berger lipid parameters".<br>
>>>>> Delete line ";; parameters for lipid-GROMOS interactions." and its<br>
>>>>> subsequent<br>
>>>>> line, change HW as H of [ nonbond_params ]<br>
>>>>><br>
>>>>><br>
>>>>> 5) Generate .tpr for POPC<br>
>>>>> grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr -maxwarn 1<br>
>>>>> (change OW1, HW2, HW3 to OW, HW and HW2 respectively)<br>
>>>>><br>
>>>>><br>
>>>>> 6) Remove periodicity<br>
>>>>> trjconv -s em.tpr -f popc128a.pdb -o popc128a_whole.gro -pbc mol -ur compact<br>
>>>>> (at command prompt select 0)<br>
>>>>><br>
>>>>><br>
>>>>> 7) Oriant the protein within the same coordinate as written in end of<br>
>>>>> popc128a_whole.gro<br>
>>>>> editconf -f 3gd8-mod-processed.gro -o 3gd8-mod-processe_newbox.gro -c -box<br>
>>>>> 6.23910 6.17970 6.91950<br>
>>>>><br>
>>>>><br>
>>>>> 8) Pack lipid around protein<br>
>>>>> cat 3gd8-mod-processe_newbox.gro popc128a_whole.gro> system.gro<br>
>>>>><br>
>>>>> Remove unnecessary lines (the box vectors from the KALP structure, the<br>
>>>>> header<br>
>>>>> information from the DPPC structure and update the second line of the<br>
>>>>> coordinate file (total number of atoms) accordingly.<br>
>>>>><br>
>>>>> 9) Modify topol.top to add positional restrain on protein<br>
>>>>><br>
>>>>> ; Include Position restraint file<br>
>>>>> #ifdef POSRES<br>
>>>>> #include "posre.itp"<br>
>>>>> #endif<br>
>>>>><br>
>>>>> ; Strong position restraints for InflateGRO<br>
>>>>> #ifdef STRONG_POSRES<br>
>>>>> #include "strong_posre.itp"<br>
>>>>> #endif<br>
>>>>><br>
>>>>> ; Include DPPC chain topology<br>
>>>>> #include "dppc.itp"<br>
>>>>><br>
>>>>> ; Include water topology<br>
>>>>> #include "gromos53a6_lipid.ff/spc.itp"<br>
>>>>><br>
>>>>> &<br>
>>>>> Genrate new positional restraint<br>
>>>>> genrestr -f 3gd8-mod-processe_newbox.gro -o strong_posre.itp -fc 100000<br>
>>>>> 100000<br>
>>>>> 100000<br>
>>>>> for system (protein + ligand)<br>
>>>>> Add a line "define = -DSTRONG_POSRES" to .mdp file<br>
>>>>><br>
>>>>><br>
>>>>> 10) addion POPC 128 to topol.top<br>
>>>>><br>
>>>>><br>
>>>>> 11) Scale down lipid<br>
>>>>> perl <a href="http://inflategro.pl" target="_blank">inflategro.pl</a> system.gro 0.95 POPC 0 system_shrink1.gro 5<br>
>>>>> area_shrink1.dat<br>
>>>>><br>
>>>>><br>
>>>>><br>
>>>>> 12) Solvate with water<br>
>>>>><br>
>>>>> Copy vdwradii.dat from Gromacs top to working directory and change the value<br>
>>>>> of<br>
>>>>> C from 0.15 to 0.375(to avoid addition of water in lipid hydrohphobic core)<br>
>>>>><br>
>>>>> genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro -p<br>
>>>>> topol.top<br>
>>>>><br>
>>>>><br>
>>>>> Upto 11th step .gro file is OK conatin protein resid 32-254, ligand 1LIG,<br>
>>>>> POPC<br>
>>>>> resid 1-128 and solvent<br>
>>>>><br>
>>>>> After 12th step in gro file protein is there 32-254, Ligand 1LIG but POPC<br>
>>>>> resid<br>
>>>>> 2-128 because resid 1 of POPC is converted to 1LIG though all cordinate and<br>
>>>>> atom<br>
>>>>> name are same of 1POPC in 1LIG.<br>
>>>>><br>
>>>>><br>
>>>>><br>
>>>>> Anybody please suggest me why this change in rename is occuring.<br>
>>>>><br>
>>>><br>
>>>> Based on the description, you say in step (3) that you add "LIG 1" to the end<br>
>>>> of<br>
>>>> [molecules], but then in (12) you give the order as protein, ligand, then<br>
>>>> POPC.<br>
>>>> The order of the coordinate file and [molecules] must match, otherwise<br>
>>>> funny<br>
>>>> things happen. If you have protein, ligand, and POPC, you must list the<br>
>>>> moleculetype names in that order in [molecules].<br>
>>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
>>><br>
>>> Thanks for reply<br>
>>> In step 3 I added "LIG 1" to the end of [molecules] because when I used<br>
>>> command "pdb2gmx -f 3gd8-mod.pdb -o 3gd8-mod-processed.gro -water spc" to<br>
>>> generate topol.top it already contain "Protein_chain_A 1" in [molecules] so I<br>
>>> added only "LIG 1"<br>
>>><br>
>>><br>
>>> This is end of topol.top after solvation<br>
>>><br>
>>> [ molecules ]<br>
>>> ; Compound #mols<br>
>>> Protein_chain_A 1<br>
>>> LIG 1<br>
>>> POPC 128<br>
>>> SOL 1829<br>
>>><br>
>>><br>
>>><br>
>><br>
>> OK, that makes sense. Did InflateGRO remove any lipids? If it did, that is not<br>
>> reflected correctly in the topology.<br>
><br>
><br>
><br>
><br>
> No it did,nt. After using InflaterGRO it tells 64 lipid in uper leaflet and 64<br>
> in lower leaflet so there are total 128 lipid before and after scaling down.<br>
><br>
<br>
That's bizarre. Even the smallest protein should cause some lipid overlap,<br>
unless your initial scaling factor was enormous. Also note that InflateGRO will<br>
indeed report that there are 64 lipids per leaflet, but only later in the screen<br>
output will it state whether or not it is removing any lipids.<br>
<br>
The only feasible source of error I can think of is that there is a mismatch<br>
between the coordinate and topology files, but given the information at hand I<br>
can't see its origin. Check all your steps again carefully, verify the contents<br>
of the coordinate file using external means (counting via grep, etc), and if all<br>
else fails, start again, making sure of each step along the way.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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End of gmx-users Digest, Vol 98, Issue 42<br>
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